Questions about bayesTyperTools combine

[zhiyongli1995]

Hi,

First, When I using bayesTyper cluster, I got this error ERROR: Variants on the same position need to be multi-allelic; multiple variants observed on position "537199" on contig "chr2", then I trying to use bayesTyperTools combine to convert it. However, in my VCF file there are many duplication type variation , after converting, the ref allele changed to alt allele. Is that a BUG?
Another question is can bayesTyper support the duplication genotype? If it can do, the first question more confuse me!

For example:
Before combine:

#CHROM  POS     ID      REF     ALT
chr2    3106    DUP6079 CTTCGGTCCTGCGGAAGGCAAAGGTACAAGCGTGATG    .
chr2    6812772    DUP6080 CTTCGGTCCTGCGGAAGGCAAAGGTACAAGCGTGATG    .
chr2    6812772    DUP6081 CTTCGGTCCTGCGGAAGGCAAAGGTA    .

After combine:

#CHROM  POS     ID      REF     ALT
chr2    3106    .    C     CTTCGGTCCTGCGGAAGGCAAAGGTACAAGCGTGATG
chr2    6812772    .    C    CTTCGGTCCTGCGGAAGGCAAAGGTACAAGCGTGATG,CTTCGGTCCTGCGGAAGGCAAAGGTA

[jonassibbesen]

Hi,

It is not supposed to change the REF allele to ALT for duplications. I am looking at your vcf before combine and it looks like all the ALT sequences are missing. Is this correct? If so then it might be a bug. Would it be possible for you to share a vcf with the above lines and the header?

Thanks,

Jonas

[zhiyongli1995]

Hi Jonas,

Sorry the ALT sequences should not be missing, that is my fault. However, the REF allele really been changed.
Here are my my vcf files head lines.

Best regards,
Zhiyong

My original vcf head lines:

##fileformat=VCFv4.3
##fileDate=20210112
##source=syri
##ALT=<ID=SYN,Description="Syntenic region">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=TRANS,Description="Translocation">
##ALT=<ID=INVTR,Description="Inverted Translocation">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INVDP,Description="Inverted Duplication">
##ALT=<ID=SYNAL,Description="Syntenic alignment">
##ALT=<ID=INVAL,Description="Inversion alignment">
##ALT=<ID=TRANSAL,Description="Translocation alignment">
##ALT=<ID=INVTRAL,Description="Inverted Translocation alignment">
##ALT=<ID=DUPAL,Description="Duplication alignment">
##ALT=<ID=INVDPAL,Description="Inverted Duplication alignment">
##ALT=<ID=HDR,Description="Highly diverged regions">
##ALT=<ID=INS,Description="Insertion in non-reference genome">
##ALT=<ID=DEL,Description="Deletion in non-reference genome">
##ALT=<ID=CPG,Description="Copy gain in non-reference genome">
##ALT=<ID=CPL,Description="Copy loss in non-reference genome">
##ALT=<ID=SNP,Description="Single nucleotide polymorphism">
##ALT=<ID=TDM,Description="Tandem repeat">
##ALT=<ID=NOTAL,Description="Not Aligned region">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position on reference genome">
##INFO=<ID=ChrB,Number=1,Type=String,Description="Chromoosme ID on the non-reference genome">
##INFO=<ID=StartB,Number=1,Type=Integer,Description="Start position on non-reference genome">
##INFO=<ID=EndB,Number=1,Type=Integer,Description="End position on non-reference genome">
##INFO=<ID=Parent,Number=1,Type=String,Description="ID of the parent SR">
##INFO=<ID=VarType,Number=1,Type=String,Description="Start position on non-reference genome">
##INFO=<ID=DupType,Number=1,Type=String,Description="Copy gain or loss in the non-reference genome">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr2    1       NOTAL1  N       <NOTAL> .       PASS    END=3105;ChrB=.;StartB=.;EndB=.;Parent=.;VarType=.;DupType=.
chr2    3106    DUP6079 N       <DUP>   .       PASS    END=11964;ChrB=chr2;StartB=71745602;EndB=71754416;Parent=.;VarType=SR;DupType=copyloss

My vcf after convert:

##fileformat=VCFv4.2
##ALT=<ID=CPG,Description="Copy gain in non-reference genome">
##ALT=<ID=CPL,Description="Copy loss in non-reference genome">
##ALT=<ID=DEL,Description="Deletion in non-reference genome">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=DUPAL,Description="Duplication alignment">
##ALT=<ID=HDR,Description="Highly diverged regions">
##ALT=<ID=INS,Description="Insertion in non-reference genome">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=INVAL,Description="Inversion alignment">
##ALT=<ID=INVDP,Description="Inverted Duplication">
##ALT=<ID=INVDPAL,Description="Inverted Duplication alignment">
##ALT=<ID=INVTR,Description="Inverted Translocation">
##ALT=<ID=INVTRAL,Description="Inverted Translocation alignment">
##ALT=<ID=NOTAL,Description="Not Aligned region">
##ALT=<ID=SNP,Description="Single nucleotide polymorphism">
##ALT=<ID=SYN,Description="Syntenic region">
##ALT=<ID=SYNAL,Description="Syntenic alignment">
##ALT=<ID=TDM,Description="Tandem repeat">
##ALT=<ID=TRANS,Description="Translocation">
##ALT=<ID=TRANSAL,Description="Translocation alignment">
##INFO=<ID=ChrB,Number=1,Type=String,Description="Chromoosme ID on the non-reference genome">
##INFO=<ID=DupType,Number=1,Type=String,Description="Copy gain or loss in the non-reference genome">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position on reference genome">
##INFO=<ID=EndB,Number=1,Type=Integer,Description="End position on non-reference genome">
##INFO=<ID=Parent,Number=1,Type=String,Description="ID of the parent SR">
##INFO=<ID=StartB,Number=1,Type=Integer,Description="Start position on non-reference genome">
##INFO=<ID=VarType,Number=1,Type=String,Description="Start position on non-reference genome">
##contig=<ID=chr2,length=244442276>
##fileDate=20210112
##source=syri
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr2	3106	DUP6079	CTTCGGTCCTGCGGAAGGCAAAGGTACAAGCGTGATGCGAAAGCAAATGACAGGTTCACGTGAACAGTACAGAGGTACTGTTCATCTATTTATAGGCACAGGTCGCAGCCTGTGACAAATTACAATTATGCCCCTTGCGAAAGTTTATAGCATTAACTCAGACTCATATGTATAAAAAGGTCATTCTATCTCTATGTCGGTTTAAAAACGCCGAAGCTCCATGAAAAGGGACCTTCGGCCATCTCTTGGAGACGACTTCAGCCGAAGCTGCTTCTTCATGTGAGACCTTCGGCGCACCGAAGCACGACCCCAACAGTAGCCCCTTTCGCGGTGCTAGATCGTTCTTCGTAACGAGCTTGACCCGTGAAAAAAGCCTCTTCAGCTTCGGGAAGCCGAAGGTCCAAAAAACACCTTCCCTGAGCTCGTTGCGGAGAAACGATCCGACTTCCGAGCGCGTGTCGGTCCCACCTTGCAGAGTTACTGTTTGATCCTTGCGGTCCACTGCGCAGCGGGTACAAGTTACGGCGCGCCTGGTGTAACAATTCCGCCGCTTCGCCTTGTTTCCTGCAGTACTATATAAACAAGCAGGTAGGTGTAAAGTTACCACAGCATTCATTGCTATTTGCACTGTTTTGCTGCCGAAATTTTCCATCATAGCCGAAGCTTAAATCCCAAAATCGAACGAAGGTCCGTCTCGACACTTGCTTCGTCAGAAAGAAGAGCTTCGGAGAGAAGAAAAAAGTAAAAAGTTTCTGACTTCCCAAACTTAAAATCAAATGGCGAGAATTCGATCTACTGCCAAAGTTGTACGCGAGGGAGACGAAGCCGAAGGTTCAAACACTGTGCCCATCTCCGAAGCGATGCAGCGCTCCGGTCTAGTGGCTGCGGAAGAGAGGCCTGGTACCGAAGCAAACCCGACAACAGCCGAAGAAGAAAACATTGATGGGACTGACTCCGGAGATGACTACCACATGTCTACACCCAGCAAGCCCAGTCACCTGGATTTTGGAAAATCAACTGTTTCAAAGGCTGACCTTGCGAAGATGATAAAGGCAGGTTTTTTCAAAGAAGATCAAAAAAAGCTACTTCGCTTCGGAGGAGAGGAGACTACCCCGAAGCCAGAGAAGGATGAGATTGTAATTTTCAAAAGCTTTTTAAAAGCTGGGCTGAGATTTCCTCTTCATGGAATTATTGGAGATGTGTTGCAAAAGTTTGGCATTTATTTTCACCAATTGACTCCTAACGCCATTGTTAGGCTTAATGTTTATATTTGGGCTCTCCGAAGCCAAGCTGTGGAACCGTTTGCCGACAGCTTCTGCCGAGCGCACGAATTACATTACCAAACGAAGGCCAGAGCAGACGGACTACATGATAATTTCGGCTGTTACAATTTTGCCTACCGGAAGACAACAAAGTGTCCTGTTATCAGCTACCGGAGCAAATGGCCAGCAGGCTGGAAGTCTGAGTGGTTCTACGTAAAAGTTGACGAAGACAGAGAAAAATTGATACAAAGTCCTCTGGAATTAATCTTCGGAGAGACAAGGCCACACTGCCACATCGGCGATTTAAAGGGTCCTACCTGGGCCGCTCTGGGTGAATTCGAAATTATTTCAGAACATATTGGCACCAGGGATCTGGTTCAGGAATTTTTGGCATTCAGAGTTTTCCCTACTTTAAAAGAGTGGGAGATGCCGAAGCTGGAGGGAGAGAAGAAGGAGGGGGAGCTTGTTCGTCTGCCTTATCACTTTAAATTCAAGAAGTACTTTAAGAAACCCTGCAAAGAGTGGTTGGACACAGTTGAGACAATGTGCAATGAAATCTTGGGGAACTACTCCAAAAAGGAGGATCAATTAATGACAGCAGCCTTCGGCACCCGACCGAAGCGAAGGCTGAACCGAGTATTCGATGCCCTGGGCTTCGAGTATCCAGACTATGAGCAGTTGAATAAGGGTGCCGAAGGCCACAAAAGAAAAAGAGTGACTGAAATTCTGACGAAGGATGAAGAGCAACCAGCAGCAGAGAAGAAAATTCCAAAGAAAAGGAAAATATCAACTCCGAAACGGAAAATATCCAAAGAAGAGAAAACCCCCACACCGCCTTCTACTAGCGACATAGAAGAAATTTTAAAGGTAATGACTGAACCCATGCCTACGAAGCTAAGTCCACTAGGGCTCCAACTGACGAAGCTTTTTCGAAAGGTGGACGAGCCGGATCAGACGAAGACAAGCAAACCCAAGCGGCAAAGAATCATTGCGGTAACTGAAGTTATCGATAAGACGCCGCCAAGGGCGTCAATCCAAAAAACGGCAGCTGCCGAAGGTGCAGCAATTGTCGAAGGCGTAGCTTCGGGGGTCGCGGCTACCGAAGCCGCTACAGCCGAAGATACAAACTTAAAAACCACGATTACGAATATCAACAAGATTTTGGAAGACATGGCCGCGGAAGAAACTGGTGCTACTTCTGAAAAAACCATGGCCACAGTGCCTGAAAAAGGAAAAGAAATAGCCGAAGACCCTTCGGATGACGAAGCATACACTTTCCAGAACTTAGTTGGGCAAAAACTGACGAAGGAGGAAATAGAAGAACTTAAAGAATACGCCAAGTCTTGCGGGTACAAGTCAGGTGCCCTCCTATTTGGGGGTGTAGATGATGAACAACTGGGCTGCATCCGGGACTCAGCTGGGGCTAAGGTCATCGGTACTTTATCAAAGAGTATCGGTTTTCCGAAGCTGGAGTCAGACATCAGCCGCTACCGACGACAACATGTCGTTGGTAGTTTATTTTATTCTAACTTCAAGGTGAATGACTTGTTTCTTAACCTTTATTGCTTCTAATAAAAACATGACTGACGAAGGTTGTGTTTGTGTAGAGTATGCTATTGAGCAAGGCTTTGCAAATGCAGCAGGATCTTGAAGATAAAAAGCATGAAGTTATAATTGAAAATTTGGAAAACAAAATAAAGGAACAATCAGATGCTTTTGAGAAAAAGAGCTTCGAACTCCAGGCAGCCGAAGGTTTACTGGCGGAAGCTGAAGCAAAAATATTAGAACTGAACACGAAGCTTCTCCGCCAGTCTGAGCAGTTCGAACAAGAAAAACAAGATCTCAATGCAAAACTTGAAGCCGAAGCTCAGCAAAATTCGGATTTGAGAAAATTATTGACAAATCTTCAAGAAAAATGCCTAGAATTTAGCAACAAGTGCATTCAGCGACTAAGAAAGATTTTTCATTCGGTTGGAGCTAGCAGCGAAAAATTTACCCCCTCAGCTGAAGACCTACCACAAACCTTCGAACACATTGAGGGGGAAATTGACGAGCTCGACGAAGTCATAGCTGGGCATGGTGATTTCTGTGCCTGGGTAGCTTCTCGAGGGACTGCTGCAGCCTTCATGAAGGCTGGCTGTGAACATGGAAAAGTTGTTAACAGACCCACCTTCGCCTTATCTCCATCAATCCTGGATGATATGCCTGACCTTGCCCGAAGTATCTCCAACAGATTTATAAAAATGATATGGACAAAAGGCGGGCGGGAGAAGGCTGGAGATGAAGCACGAAGCCATCTTGAACCAGTAAGAGATAATACTTCGTACTTACCTTTTTCTTTGCACTTGATTTTTACTCACGGTTCCTTGATTTATGTAGGATGACGAAGGTGAAGATGATGCCTAAATTATGTCGTCGAAGCTGAAACTTAATGAAGATCAGTAGAAGTGTACTGTAGGAAAACTCAGGATATTTTTGTAACAATCCTTGTAAATACAACTAGACTATCTTCAAGGAACTTTGTACATACCTTGCAATGTATTCTTACCCTCTGCTTGAAGCGCTTTGATGTGGACGAAACCAGTATTTTGAGCCGAAGGCGAAAAACACCTTCCCTTCTTTTCGTACACAACGAAGCTTTAAAAGGTCGCTTCCTCTTTTTGCCGAAGCTTTGCTTTTTTGTACATGAAAACTACTTCTCCTTTCTGCCGAAGCTTTTCTTTACAAAACATAAAAAACTACTTCTCTTTTCTGCCGAAGCTTTCCTTTACATGACAAAACATAAAAGACTACTACTCTTTTGCACAACGATTCGTAAAAATCCAGTTCTCCCTTATACTGAACTTTTCCTTGTGCCAAAGCAACGGAACTTTTCACTTTTGCACACAACATAGCGTAATAAGTCATAAAAGGTACTTCTCCGAAGCTTTTTTGCCGAAGCAGCCACTTGGGAACACAAATGCTATGAATGAATGCTTATGCATGCGAATGTTATGATGTAATGTAATGCACGAATGAATGTCCGAAGCATATGTCCGAAGCCATATTGTCAGCCATTACTTGAAAACAACCACACATTAGCTCTGCATTCCCTTAGGAACGACTTTGGAGCTTCTTCGCCTCTTACTTAGGCAATATCAGCGTTGACTTTTCGCTGTAAGCTCTGCATCCCCTTAGGGACGTCTTTGGAGCTTCTTCGTCTTTTACTTAGACGGTATAAGCTCTGCATTCCCTTGGGAACGTCTTTGGAGCTTCTTCGTCTTTTACTTAGACGGTATAAACTCTGCATTCCCTTAGGAACGTCTTTGGAGTTTCTTCGCCTTTTACTTAGGCGGTATAAGCTCTGCATTCCCTTGGGAACGTCTTTGGAGCTTCTTCTCTTTTTTCTTTTTCAGTTTCTGCACTCGATGGTGCGTTCTCAGCTGTTACATTTACATTTTTTGGGGGATTTCGCTCTTATAAGACTAAAAAAGGAAATTACACATGATGGCCCTATTAAAAACCTTTCTCCCCCTTCGGAAAGGAAAAGGGTGCCATGAAAATGAAAAGAAAAAGCATAAAAAATTACATCATATTATACATAGTATCGCCGAAGCTCATCCGCATTCCAAGACCTTGGAATTTCGTTGCCATCCATGTCCTTCAATCTGTATGATCCAGGCCTTGACGAAGATACTACTAAGAATGGTCCTTCCCATTTCAACTGTAGCTTACCCACTGTATCTGGGTTAGCCACTCTCCGAAGCACCAAGTGTCCCGGCTCAATATTTTTTAGCCGGACTTTTCTATCTCGCCATTTGACTGTTTCAGCCTGATATTTATTAATATTCTCCACGGCCTGAAGCCTGATCCCCTCTAAAGCATCTTTTTCCACAAGATAAGCATCTTCGGGGCCTGATTCTGCCGAAGCTACTACTCTTACTGACCCAGCTTTTGCTTCCTCCGGAGTTATTGCTTCGTCACCGAATAATAATTTGAATGGGGTAAAGCCTGTAGACCTTGATGTTGTTGTATTGTGGCTCCACACCACTTTGATTAACTGATCTGGCCACTTTCCCCTGGGTTGATTGAAGATTAACTTCATTATTCCTGTCATTATAATGCCGTTGGCCCTTTCAACGAGCCCATTTGACTCCGGATGCCTGACTGACGCAAAATGGATCTTCGTTCCGATTTGATTACAGAAGTCTCTGAAAGCTTCGGAGTCAAACTGCGTTCCATTATCTACAGTAATTGCCTTCGGTACCCCGAAGCGACAGACAATATTCTGCCAGAAAAACTTTTGGACAGTGGCTGAAGTTATTGTGGCCAATGGCTTCGCCTCAATCCACTTGGAAAAATACTCCACAGCCACTATAACATATTTTAGATTCCCTTGAGCCGGTGGTAATGGGCCCAACAAGTCAAGGCCCCACCTTTGCAATGGCCAGATGGGTTGTATCAGCTGTGTTAAAGACGAAGGTTGTTTTTGATCTCTTGCACATTTCTGACAACCTTCGCACTTTTGCACTAACTCCGCTGCATCCGAAGCTGCCTTCGGCCAATAAAATCCTTGGCGGAAGACTTTCCCAAGTAATGGCCTAGATCCAATGTGGGATCCACACAGGCCTGCATGTATCTCTTTCATCAACTCTATACCTTCGGCTCTAGATAAGCACTTGAGCAGCGGAGCACAAACTCCATGTTTGTATAATTCCCCTTCTATCATGACATACGGACGAGCTCTTGCCTCTATTCTTTTATTGTAAGCTTCGTCATCTGAAAGGGACTTACCCTGAAGGTAAGAGATTATTTCAGTTCTCCAATCTTCGCTGTAAACAGGAGATATGTTGAGGACTGCTCTTTCAAGGAGCTCCACTGAAGGTGCCTTTATTGTTTCGAAAAACACATCCGAGGGTAACGGCAGCCCCTGTGCCGCAGACTTAGCTAGCAAATCAGCATGCTCATTTTGTCCTCGAGGAATATTCTTGACCGAGAATCCTTCGAAGGATGCCTCGATCCTTCGGACCGTATCTAGATACTTTTCAAGCTTCGGATCTTTAGCTTTGCAACTTTTGTCAACATGACCCGAAACCACCTGGGAATCAGTTTTAAGAATTGCCCTTCTGATTCCCATTGCCTTTAATTTCCGAAGGCCCAAAAGCAGGGCTTCGTACTCAGCAATATTGTTCGTGCAGCTGAAATCAAGTCTTGCTGCGTAACAAGTTTTGACATTGGATGGTGAAACCAACACAGCAGCTGCACCTGCTCCGAAGATTCCCCAAGAGCCATCACAAAACACTGTCCACACTTCGGCATCTTTATTTGCTTCTTCATCCTTCGCCCCTGGTGTCCAGTCGGCAATGAAATCTGCCAATGCTTGAGACTGGATCGAAGATCTATGCACATAATCAATGTAAAATTCGTTGAGCTCTGCAGCCCATTTCCCAATCCGTCCAGTAGCTTCTCTATTTCTCATTATATCCTTCAACGGCTGCGAAGAAGGAACAATGATATTGTATGCCTGAAAATAATGCCGAAGCTTCCTGGATGCCATTAAAACGGCATATAATACCTTCTCCAGCTCTGTATAATTTTTCTTTGAGACACTAAGGACCTCAGATACAAAGTACACTGGAACTTGCTTCTTAAGCTGGCCATAAAGCTTCTCCTGGACAAGCGCCGCACTTACTGCTGAGTGCGAAGCTGCCACATATAACAACAGAGGAGCCCCTGGCGTTGGCGGAGTTAATGTTGTGAGATCTATCAAGTATTGCTTCAACTCTTCGAAGGCTTTTTGTTGACTTGGGCCCCATTGAAAGACTTCGGCTGACTTCAGCACCTCGAAGAATGGTAAGTTTCTTTCTGCTGATCTGGATATAAATCTGTTGAGAGATGCTAGCCTTCCTGTCAATCTTTGGGCCCCTTTTCTTGTAGTTGGTGGCTCCATTCGAAGTATAGCTTCGATTTTATTTGGATTAGCTTCGATTCCCTTTGTTGAAACTAAGCATCCAAGAAATTTACCCTTCTTTACTCCGAAGACACATTTCTCTGGATTCAGCTTCAGACCAGCTTGTCTGAAGCTGGCGAAGGTCTCCTGCAGATCAGCAATATGGTCCTCTTGCTTCGTGCTTTTGACGATAATGTCATCAACATAGGTCAACACATTTCTACCTATTTGAGACTGGAGAACCTTCGCAGTCATTCTGCTGAAACTTCCTCCAGCGTTTTTGAGCCCCTCAGGCATCCGAAGATAGCAATACGTGCCACTTGGAGTTATGAAGCTAGTTTTCGGCTCATCTTCCTTTTTCATCCAGATTTGATGATATCCTGAGTAACAGTCCAAGAGACTCATGAGCTCTGAAGAAGCTGCTGCATCGACTAGAGAGTCTATCCTTGGCAACGGGAATTCGTCCTTCGGACAAGCTTTGTTGAGATCTGTGAAATCGATACACATTCTCCACTTGCCATTGGCCTTCTTCACCATAACAGTGTTAGCTAGCCACTCTGGGTACTTCACTTCTCTGATAACTCCTGCACTGAGGAGTCTTTTTACTTCGTTGCGAGCCCCTTCGGCCTTGTCATCAGACATTTTCCGAAGCCTCTGCTTTCGGGGTCTAAAGGATGGGTCAACATTGAGCGAATGTTCAATAACATCCCGGTTTACTCCACAGAGATCATTAGCCGACCATGCAAAAACATCTTTGTTGTTGAATAAAAACCTTATCAAGGTTTTCTCCTGGTCTTCAGATAACTGCGAGCCCAACAGCACCTTCTGATCTGCTATGTCTTCGCACAATAGCATGGGCTTCGGCTGATCAGCCGAAGCTGCTTTTTCCCTCCTGAACTTGTACTGTTCACAAGCTTCAACTCCATCTATATTATGGATTGCCTTGGAATCAGTCCAGCTTCCTTCGGCCCTTCTGGCAGCTTCCTGACTCCCATGAATAGCAATAGGCCCTTGGTCCGAAGGTATCTTCATGCAGAGATAAGCTGGGTGAAGAATTGCTTCAAAAGCATTTAGGGTACCACGACCAATGATGGCGTTGTAGGGGTATTCCATGTCAACAATATCAAACACAATTTGCTCAGTCCTTGTGTTATTAACAAATCCGAAGGTTACCGGCATGGTAATCTTCCCGAGTGCCACAATCTGTCGCCCTCCGAAGCCACAAAGAGGGTGCGTAGCATCATGAATCTTGTCTTCAGGCTCTTGCATCTGTCTGAAGGCTTTGGCAAATATGATGTCAGCTGCACTGCCTGTGTCGACCAAGACATTGTGGACCAGAAATCCTTTGATAACACAAGAGATAACCATGGCATCATTGTGTGGGTAATCTTTAAGCTGAAGGTCCTCTTGGGAGAAGGTAATTGGAATGTGAGACCATTTTGACTTAATGAAGGGTCCCTGCACGCCAACATGCTGCACCCTTCTCTGAGCCTCCTTCTTCTGCCTTTTGTTAGCTGGCTCTGAGCAAGAACCGCCTGTTATCGGGAGCACCAGCTTCGAAGCCGAAGCAGCTCCAGCTTGAGTGTTGAACGAAGCCATCAGCTCAGAAAGGTGGAAGTGAGTTGACCGGAGGTGGGCGCCAATGTTGGGGACTTGTTCTCAAATGCT	CTTCGGTCCTGCGGAAGGCAAAGGTACAAGCGTGATGCGAAAGCAAATGACAGGTTCACGTGAACAGTACAGAGGTACTGTTCATCTATTTATAGGCACAGGTCGCAGCCTGTGACAAATTACAATTATGCCCCTTGCGAAAGTTTATAGCATTAACTCAGACTCATATGTATAAAAAGGTCATTCTATCTCTATGTCGGTTTAAAAACGCCGAAGCTCCATGAAAAGGGACCTTCGGCCATCTCTTGGAGACGACTTCAGCCGAAGCTGCTTCTTCATGTGAGACCTTCGGCGCACCGAAGCACGACCCCAACAGTAGCCCCTTTCGCGGTGCTAGATCGTTCTTCGTAACGAGCTTGACCCGTGAAAAAAGCCTCTTCAGCTTCGGGAAGCCGAAGGTCCAAAAAACACCTTCCCTGAGCTCGTTGCGGAGAAACGATCCGACTTCCGAGCGCGTGTCGGTCCCACCTTGCAGAGTTACTGTTTGATCCTTGCGGTCCACTGCGCAGCGGGTACAAGTTACGGCGCGCCTGGTGTAACAATTCCGCCGCTTCGCCTTGTTTCCTGCAGTACTATATAAACAAGCAGGTAGGTGTAAAGTTACCACAGCATTCATTGCTATTTGCACTGTTTTGCTGCCGAAATTTTCCATCATAGCCGAAGCTTAAATCCCAAAATCGAACGAAGGTCCGTCTCGACACTTGCTTCGTCAGAAAGAAGAGCTTCGGAGAGAAGAAAAAAGTAAAAAGTTTCTGACTTCCCAAACTTAAAATCAAATGGCGAGAATTCGATCTACTGCCAAAGTTGTACGCGAGGGAGACGAAGCCGAAGGTTCAAACACTGTGCCCATCTCCGAAGCGATGCAGCGCTCCGGTCTAGTGGCTGCGGAAGAGAGGCCTGGTACCGAAGCAAACCCGACAACAGCCGAAGAAGAAAACATTGATGGGACTGACTCCGGAGATGACTACCACATGTCTACACCCAGCAAGCCCAGTCACCTGGATTTTGGAAAATCAACTGTTTCAAAGGCTGACCTTGCGAAGATGATAAAGGCAGGTTTTTTCAAAGAAGATCAAAAAAAGCTACTTCGCTTCGGAGGAGAGGAGACTACCCCGAAGCCAGAGAAGGATGAGATTGTAATTTTCAAAAGCTTTTTAAAAGCTGGGCTGAGATTTCCTCTTCATGGAATTATTGGAGATGTGTTGCAAAAGTTTGGCATTTATTTTCACCAATTGACTCCTAACGCCATTGTTAGGCTTAATGTTTATATTTGGGCTCTCCGAAGCCAAGCTGTGGAACCGTTTGCCGACAGCTTCTGCCGAGCGCACGAATTACATTACCAAACGAAGGCCAGAGCAGACGGACTACATGATAATTTCGGCTGTTACAATTTTGCCTACCGGAAGACAACAAAGTGTCCTGTTATCAGCTACCGGAGCAAATGGCCAGCAGGCTGGAAGTCTGAGTGGTTCTACGTAAAAGTTGACGAAGACAGAGAAAAATTGATACAAAGTCCTCTGGAATTAATCTTCGGAGAGACAAGGCCACACTGCCACATCGGCGATTTAAAGGGTCCTACCTGGGCCGCTCTGGGTGAATTCGAAATTATTTCAGAACATATTGGCACCAGGGATCTGGTTCAGGAATTTTTGGCATTCAGAGTTTTCCCTACTTTAAAAGAGTGGGAGATGCCGAAGCTGGAGGGAGAGAAGAAGGAGGGGGAGCTTGTTCGTCTGCCTTATCACTTTAAATTCAAGAAGTACTTTAAGAAACCCTGCAAAGAGTGGTTGGACACAGTTGAGACAATGTGCAATGAAATCTTGGGGAACTACTCCAAAAAGGAGGATCAATTAATGACAGCAGCCTTCGGCACCCGACCGAAGCGAAGGCTGAACCGAGTATTCGATGCCCTGGGCTTCGAGTATCCAGACTATGAGCAGTTGAATAAGGGTGCCGAAGGCCACAAAAGAAAAAGAGTGACTGAAATTCTGACGAAGGATGAAGAGCAACCAGCAGCAGAGAAGAAAATTCCAAAGAAAAGGAAAATATCAACTCCGAAACGGAAAATATCCAAAGAAGAGAAAACCCCCACACCGCCTTCTACTAGCGACATAGAAGAAATTTTAAAGGTAATGACTGAACCCATGCCTACGAAGCTAAGTCCACTAGGGCTCCAACTGACGAAGCTTTTTCGAAAGGTGGACGAGCCGGATCAGACGAAGACAAGCAAACCCAAGCGGCAAAGAATCATTGCGGTAACTGAAGTTATCGATAAGACGCCGCCAAGGGCGTCAATCCAAAAAACGGCAGCTGCCGAAGGTGCAGCAATTGTCGAAGGCGTAGCTTCGGGGGTCGCGGCTACCGAAGCCGCTACAGCCGAAGATACAAACTTAAAAACCACGATTACGAATATCAACAAGATTTTGGAAGACATGGCCGCGGAAGAAACTGGTGCTACTTCTGAAAAAACCATGGCCACAGTGCCTGAAAAAGGAAAAGAAATAGCCGAAGACCCTTCGGATGACGAAGCATACACTTTCCAGAACTTAGTTGGGCAAAAACTGACGAAGGAGGAAATAGAAGAACTTAAAGAATACGCCAAGTCTTGCGGGTACAAGTCAGGTGCCCTCCTATTTGGGGGTGTAGATGATGAACAACTGGGCTGCATCCGGGACTCAGCTGGGGCTAAGGTCATCGGTACTTTATCAAAGAGTATCGGTTTTCCGAAGCTGGAGTCAGACATCAGCCGCTACCGACGACAACATGTCGTTGGTAGTTTATTTTATTCTAACTTCAAGGTGAATGACTTGTTTCTTAACCTTTATTGCTTCTAATAAAAACATGACTGACGAAGGTTGTGTTTGTGTAGAGTATGCTATTGAGCAAGGCTTTGCAAATGCAGCAGGATCTTGAAGATAAAAAGCATGAAGTTATAATTGAAAATTTGGAAAACAAAATAAAGGAACAATCAGATGCTTTTGAGAAAAAGAGCTTCGAACTCCAGGCAGCCGAAGGTTTACTGGCGGAAGCTGAAGCAAAAATATTAGAACTGAACACGAAGCTTCTCCGCCAGTCTGAGCAGTTCGAACAAGAAAAACAAGATCTCAATGCAAAACTTGAAGCCGAAGCTCAGCAAAATTCGGATTTGAGAAAATTATTGACAAATCTTCAAGAAAAATGCCTAGAATTTAGCAACAAGTGCATTCAGCGACTAAGAAAGATTTTTCATTCGGTTGGAGCTAGCAGCGAAAAATTTACCCCCTCAGCTGAAGACCTACCACAAACCTTCGAACACATTGAGGGGGAAATTGACGAGCTCGACGAAGTCATAGCTGGGCATGGTGATTTCTGTGCCTGGGTAGCTTCTCGAGGGACTGCTGCAGCCTTCATGAAGGCTGGCTGTGAACATGGAAAAGTTGTTAACAGACCCACCTTCGCCTTATCTCCATCAATCCTGGATGATATGCCTGACCTTGCCCGAAGTATCTCCAACAGATTTATAAAAATGATATGGACAAAAGGCGGGCGGGAGAAGGCTGGAGATGAAGCACGAAGCCATCTTGAACCAGTAAGAGATAATACTTCGTACTTACCTTTTTCTTTGCACTTGATTTTTACTCACGGTTCCTTGATTTATGTAGGATGACGAAGGTGAAGATGATGCCTAAATTATGTCGTCGAAGCTGAAACTTAATGAAGATCAGTAGAAGTGTACTGTAGGAAAACTCAGGATATTTTTGTAACAATCCTTGTAAATACAACTAGACTATCTTCAAGGAACTTTGTACATACCTTGCAATGTATTCTTACCCTCTGCTTGAAGCGCTTTGATGTGGACGAAACCAGTATTTTGAGCCGAAGGCGAAAAACACCTTCCCTTCTTTTCGTACACAACGAAGCTTTAAAAGGTCGCTTCCTCTTTTTGCCGAAGCTTTGCTTTTTTGTACATGAAAACTACTTCTCCTTTCTGCCGAAGCTTTTCTTTACAAAACATAAAAAACTACTTCTCTTTTCTGCCGAAGCTTTCCTTTACATGACAAAACATAAAAGACTACTACTCTTTTGCACAACGATTCGTAAAAATCCAGTTCTCCCTTATACTGAACTTTTCCTTGTGCCAAAGCAACGGAACTTTTCACTTTTGCACACAACATAGCGTAATAAGTCATAAAAGGTACTTCTCCGAAGCTTTTTTGCCGAAGCAGCCACTTGGGAACACAAATGCTATGAATGAATGCTTATGCATGCGAATGTTATGATGTAATGTAATGCACGAATGAATGTCCGAAGCATATGTCCGAAGCCATATTGTCAGCCATTACTTGAAAACAACCACACATTAGCTCTGCATTCCCTTAGGAACGACTTTGGAGCTTCTTCGCCTCTTACTTAGGCAATATCAGCGTTGACTTTTCGCTGTAAGCTCTGCATCCCCTTAGGGACGTCTTTGGAGCTTCTTCGTCTTTTACTTAGACGGTATAAGCTCTGCATTCCCTTGGGAACGTCTTTGGAGCTTCTTCGTCTTTTACTTAGACGGTATAAACTCTGCATTCCCTTAGGAACGTCTTTGGAGTTTCTTCGCCTTTTACTTAGGCGGTATAAGCTCTGCATTCCCTTGGGAACGTCTTTGGAGCTTCTTCTCTTTTTTCTTTTTCAGTTTCTGCACTCGATGGTGCGTTCTCAGCTGTTACATTTACATTTTTTGGGGGATTTCGCTCTTATAAGACTAAAAAAGGAAATTACACATGATGGCCCTATTAAAAACCTTTCTCCCCCTTCGGAAAGGAAAAGGGTGCCATGAAAATGAAAAGAAAAAGCATAAAAAATTACATCATATTATACATAGTATCGCCGAAGCTCATCCGCATTCCAAGACCTTGGAATTTCGTTGCCATCCATGTCCTTCAATCTGTATGATCCAGGCCTTGACGAAGATACTACTAAGAATGGTCCTTCCCATTTCAACTGTAGCTTACCCACTGTATCTGGGTTAGCCACTCTCCGAAGCACCAAGTGTCCCGGCTCAATATTTTTTAGCCGGACTTTTCTATCTCGCCATTTGACTGTTTCAGCCTGATATTTATTAATATTCTCCACGGCCTGAAGCCTGATCCCCTCTAAAGCATCTTTTTCCACAAGATAAGCATCTTCGGGGCCTGATTCTGCCGAAGCTACTACTCTTACTGACCCAGCTTTTGCTTCCTCCGGAGTTATTGCTTCGTCACCGAATAATAATTTGAATGGGGTAAAGCCTGTAGACCTTGATGTTGTTGTATTGTGGCTCCACACCACTTTGATTAACTGATCTGGCCACTTTCCCCTGGGTTGATTGAAGATTAACTTCATTATTCCTGTCATTATAATGCCGTTGGCCCTTTCAACGAGCCCATTTGACTCCGGATGCCTGACTGACGCAAAATGGATCTTCGTTCCGATTTGATTACAGAAGTCTCTGAAAGCTTCGGAGTCAAACTGCGTTCCATTATCTACAGTAATTGCCTTCGGTACCCCGAAGCGACAGACAATATTCTGCCAGAAAAACTTTTGGACAGTGGCTGAAGTTATTGTGGCCAATGGCTTCGCCTCAATCCACTTGGAAAAATACTCCACAGCCACTATAACATATTTTAGATTCCCTTGAGCCGGTGGTAATGGGCCCAACAAGTCAAGGCCCCACCTTTGCAATGGCCAGATGGGTTGTATCAGCTGTGTTAAAGACGAAGGTTGTTTTTGATCTCTTGCACATTTCTGACAACCTTCGCACTTTTGCACTAACTCCGCTGCATCCGAAGCTGCCTTCGGCCAATAAAATCCTTGGCGGAAGACTTTCCCAAGTAATGGCCTAGATCCAATGTGGGATCCACACAGGCCTGCATGTATCTCTTTCATCAACTCTATACCTTCGGCTCTAGATAAGCACTTGAGCAGCGGAGCACAAACTCCATGTTTGTATAATTCCCCTTCTATCATGACATACGGACGAGCTCTTGCCTCTATTCTTTTATTGTAAGCTTCGTCATCTGAAAGGGACTTACCCTGAAGGTAAGAGATTATTTCAGTTCTCCAATCTTCGCTGTAAACAGGAGATATGTTGAGGACTGCTCTTTCAAGGAGCTCCACTGAAGGTGCCTTTATTGTTTCGAAAAACACATCCGAGGGTAACGGCAGCCCCTGTGCCGCAGACTTAGCTAGCAAATCAGCATGCTCATTTTGTCCTCGAGGAATATTCTTGACCGAGAATCCTTCGAAGGATGCCTCGATCCTTCGGACCGTATCTAGATACTTTTCAAGCTTCGGATCTTTAGCTTTGCAACTTTTGTCAACATGACCCGAAACCACCTGGGAATCAGTTTTAAGAATTGCCCTTCTGATTCCCATTGCCTTTAATTTCCGAAGGCCCAAAAGCAGGGCTTCGTACTCAGCAATATTGTTCGTGCAGCTGAAATCAAGTCTTGCTGCGTAACAAGTTTTGACATTGGATGGTGAAACCAACACAGCAGCTGCACCTGCTCCGAAGATTCCCCAAGAGCCATCACAAAACACTGTCCACACTTCGGCATCTTTATTTGCTTCTTCATCCTTCGCCCCTGGTGTCCAGTCGGCAATGAAATCTGCCAATGCTTGAGACTGGATCGAAGATCTATGCACATAATCAATGTAAAATTCGTTGAGCTCTGCAGCCCATTTCCCAATCCGTCCAGTAGCTTCTCTATTTCTCATTATATCCTTCAACGGCTGCGAAGAAGGAACAATGATATTGTATGCCTGAAAATAATGCCGAAGCTTCCTGGATGCCATTAAAACGGCATATAATACCTTCTCCAGCTCTGTATAATTTTTCTTTGAGACACTAAGGACCTCAGATACAAAGTACACTGGAACTTGCTTCTTAAGCTGGCCATAAAGCTTCTCCTGGACAAGCGCCGCACTTACTGCTGAGTGCGAAGCTGCCACATATAACAACAGAGGAGCCCCTGGCGTTGGCGGAGTTAATGTTGTGAGATCTATCAAGTATTGCTTCAACTCTTCGAAGGCTTTTTGTTGACTTGGGCCCCATTGAAAGACTTCGGCTGACTTCAGCACCTCGAAGAATGGTAAGTTTCTTTCTGCTGATCTGGATATAAATCTGTTGAGAGATGCTAGCCTTCCTGTCAATCTTTGGGCCCCTTTTCTTGTAGTTGGTGGCTCCATTCGAAGTATAGCTTCGATTTTATTTGGATTAGCTTCGATTCCCTTTGTTGAAACTAAGCATCCAAGAAATTTACCCTTCTTTACTCCGAAGACACATTTCTCTGGATTCAGCTTCAGACCAGCTTGTCTGAAGCTGGCGAAGGTCTCCTGCAGATCAGCAATATGGTCCTCTTGCTTCGTGCTTTTGACGATAATGTCATCAACATAGGTCAACACATTTCTACCTATTTGAGACTGGAGAACCTTCGCAGTCATTCTGCTGAAACTTCCTCCAGCGTTTTTGAGCCCCTCAGGCATCCGAAGATAGCAATACGTGCCACTTGGAGTTATGAAGCTAGTTTTCGGCTCATCTTCCTTTTTCATCCAGATTTGATGATATCCTGAGTAACAGTCCAAGAGACTCATGAGCTCTGAAGAAGCTGCTGCATCGACTAGAGAGTCTATCCTTGGCAACGGGAATTCGTCCTTCGGACAAGCTTTGTTGAGATCTGTGAAATCGATACACATTCTCCACTTGCCATTGGCCTTCTTCACCATAACAGTGTTAGCTAGCCACTCTGGGTACTTCACTTCTCTGATAACTCCTGCACTGAGGAGTCTTTTTACTTCGTTGCGAGCCCCTTCGGCCTTGTCATCAGACATTTTCCGAAGCCTCTGCTTTCGGGGTCTAAAGGATGGGTCAACATTGAGCGAATGTTCAATAACATCCCGGTTTACTCCACAGAGATCATTAGCCGACCATGCAAAAACATCTTTGTTGTTGAATAAAAACCTTATCAAGGTTTTCTCCTGGTCTTCAGATAACTGCGAGCCCAACAGCACCTTCTGATCTGCTATGTCTTCGCACAATAGCATGGGCTTCGGCTGATCAGCCGAAGCTGCTTTTTCCCTCCTGAACTTGTACTGTTCACAAGCTTCAACTCCATCTATATTATGGATTGCCTTGGAATCAGTCCAGCTTCCTTCGGCCCTTCTGGCAGCTTCCTGACTCCCATGAATAGCAATAGGCCCTTGGTCCGAAGGTATCTTCATGCAGAGATAAGCTGGGTGAAGAATTGCTTCAAAAGCATTTAGGGTACCACGACCAATGATGGCGTTGTAGGGGTATTCCATGTCAACAATATCAAACACAATTTGCTCAGTCCTTGTGTTATTAACAAATCCGAAGGTTACCGGCATGGTAATCTTCCCGAGTGCCACAATCTGTCGCCCTCCGAAGCCACAAAGAGGGTGCGTAGCATCATGAATCTTGTCTTCAGGCTCTTGCATCTGTCTGAAGGCTTTGGCAAATATGATGTCAGCTGCACTGCCTGTGTCGACCAAGACATTGTGGACCAGAAATCCTTTGATAACACAAGAGATAACCATGGCATCATTGTGTGGGTAATCTTTAAGCTGAAGGTCCTCTTGGGAGAAGGTAATTGGAATGTGAGACCATTTTGACTTAATGAAGGGTCCCTGCACGCCAACATGCTGCACCCTTCTCTGAGCCTCCTTCTTCTGCCTTTTGTTAGCTGGCTCTGAGCAAGAACCGCCTGTTATCGGGAGCACCAGCTTCGAAGCCGAAGCAGCTCCAGCTTGAGTGTTGAACGAAGCCATCAGCTCAGAAAGGTGGAAGTGAGTTGACCGGAGGTGGGCGCCAATGTTGGGGACTTGTTCTCAAATGCTTTCGGTCCTGCGGAAGGCAAAGGTACAAGCGTGATGCGAAAGCAAATGACAGGTTCACGTGAACAGTACAGAGGTACTGTTCATCTATTTATAGGCACAGGTCGCAGCCTGTGACAAATTACAATTATGCCCCTTGCGAAAGTTTATAGCATTAACTCAGACTCATATGTATAAAAAGGTCATTCTATCTCTATGTCGGTTTAAAAACGCCGAAGCTCCATGAAAAGGGACCTTCGGCCATCTCTTGGAGACGACTTCAGCCGAAGCTGCTTCTTCATGTGAGACCTTCGGCGCACCGAAGCACGACCCCAACAGTAGCCCCTTTCGCGGTGCTAGATCGTTCTTCGTAACGAGCTTGACCCGTGAAAAAAGCCTCTTCAGCTTCGGGAAGCCGAAGGTCCAAAAAACACCTTCCCTGAGCTCGTTGCGGAGAAACGATCCGACTTCCGAGCGCGTGTCGGTCCCACCTTGCAGAGTTACTGTTTGATCCTTGCGGTCCACTGCGCAGCGGGTACAAGTTACGGCGCGCCTGGTGTAACAATTCCGCCGCTTCGCCTTGTTTCCTGCAGTACTATATAAACAAGCAGGTAGGTGTAAAGTTACCACAGCATTCATTGCTATTTGCACTGTTTTGCTGCCGAAATTTTCCATCATAGCCGAAGCTTAAATCCCAAAATCGAACGAAGGTCCGTCTCGACACTTGCTTCGTCAGAAAGAAGAGCTTCGGAGAGAAGAAAAAAGTAAAAAGTTTCTGACTTCCCAAACTTAAAATCAAATGGCGAGAATTCGATCTACTGCCAAAGTTGTACGCGAGGGAGACGAAGCCGAAGGTTCAAACACTGTGCCCATCTCCGAAGCGATGCAGCGCTCCGGTCTAGTGGCTGCGGAAGAGAGGCCTGGTACCGAAGCAAACCCGACAACAGCCGAAGAAGAAAACATTGATGGGACTGACTCCGGAGATGACTACCACATGTCTACACCCAGCAAGCCCAGTCACCTGGATTTTGGAAAATCAACTGTTTCAAAGGCTGACCTTGCGAAGATGATAAAGGCAGGTTTTTTCAAAGAAGATCAAAAAAAGCTACTTCGCTTCGGAGGAGAGGAGACTACCCCGAAGCCAGAGAAGGATGAGATTGTAATTTTCAAAAGCTTTTTAAAAGCTGGGCTGAGATTTCCTCTTCATGGAATTATTGGAGATGTGTTGCAAAAGTTTGGCATTTATTTTCACCAATTGACTCCTAACGCCATTGTTAGGCTTAATGTTTATATTTGGGCTCTCCGAAGCCAAGCTGTGGAACCGTTTGCCGACAGCTTCTGCCGAGCGCACGAATTACATTACCAAACGAAGGCCAGAGCAGACGGACTACATGATAATTTCGGCTGTTACAATTTTGCCTACCGGAAGACAACAAAGTGTCCTGTTATCAGCTACCGGAGCAAATGGCCAGCAGGCTGGAAGTCTGAGTGGTTCTACGTAAAAGTTGACGAAGACAGAGAAAAATTGATACAAAGTCCTCTGGAATTAATCTTCGGAGAGACAAGGCCACACTGCCACATCGGCGATTTAAAGGGTCCTACCTGGGCCGCTCTGGGTGAATTCGAAATTATTTCAGAACATATTGGCACCAGGGATCTGGTTCAGGAATTTTTGGCATTCAGAGTTTTCCCTACTTTAAAAGAGTGGGAGATGCCGAAGCTGGAGGGAGAGAAGAAGGAGGGGGAGCTTGTTCGTCTGCCTTATCACTTTAAATTCAAGAAGTACTTTAAGAAACCCTGCAAAGAGTGGTTGGACACAGTTGAGACAATGTGCAATGAAATCTTGGGGAACTACTCCAAAAAGGAGGATCAATTAATGACAGCAGCCTTCGGCACCCGACCGAAGCGAAGGCTGAACCGAGTATTCGATGCCCTGGGCTTCGAGTATCCAGACTATGAGCAGTTGAATAAGGGTGCCGAAGGCCACAAAAGAAAAAGAGTGACTGAAATTCTGACGAAGGATGAAGAGCAACCAGCAGCAGAGAAGAAAATTCCAAAGAAAAGGAAAATATCAACTCCGAAACGGAAAATATCCAAAGAAGAGAAAACCCCCACACCGCCTTCTACTAGCGACATAGAAGAAATTTTAAAGGTAATGACTGAACCCATGCCTACGAAGCTAAGTCCACTAGGGCTCCAACTGACGAAGCTTTTTCGAAAGGTGGACGAGCCGGATCAGACGAAGACAAGCAAACCCAAGCGGCAAAGAATCATTGCGGTAACTGAAGTTATCGATAAGACGCCGCCAAGGGCGTCAATCCAAAAAACGGCAGCTGCCGAAGGTGCAGCAATTGTCGAAGGCGTAGCTTCGGGGGTCGCGGCTACCGAAGCCGCTACAGCCGAAGATACAAACTTAAAAACCACGATTACGAATATCAACAAGATTTTGGAAGACATGGCCGCGGAAGAAACTGGTGCTACTTCTGAAAAAACCATGGCCACAGTGCCTGAAAAAGGAAAAGAAATAGCCGAAGACCCTTCGGATGACGAAGCATACACTTTCCAGAACTTAGTTGGGCAAAAACTGACGAAGGAGGAAATAGAAGAACTTAAAGAATACGCCAAGTCTTGCGGGTACAAGTCAGGTGCCCTCCTATTTGGGGGTGTAGATGATGAACAACTGGGCTGCATCCGGGACTCAGCTGGGGCTAAGGTCATCGGTACTTTATCAAAGAGTATCGGTTTTCCGAAGCTGGAGTCAGACATCAGCCGCTACCGACGACAACATGTCGTTGGTAGTTTATTTTATTCTAACTTCAAGGTGAATGACTTGTTTCTTAACCTTTATTGCTTCTAATAAAAACATGACTGACGAAGGTTGTGTTTGTGTAGAGTATGCTATTGAGCAAGGCTTTGCAAATGCAGCAGGATCTTGAAGATAAAAAGCATGAAGTTATAATTGAAAATTTGGAAAACAAAATAAAGGAACAATCAGATGCTTTTGAGAAAAAGAGCTTCGAACTCCAGGCAGCCGAAGGTTTACTGGCGGAAGCTGAAGCAAAAATATTAGAACTGAACACGAAGCTTCTCCGCCAGTCTGAGCAGTTCGAACAAGAAAAACAAGATCTCAATGCAAAACTTGAAGCCGAAGCTCAGCAAAATTCGGATTTGAGAAAATTATTGACAAATCTTCAAGAAAAATGCCTAGAATTTAGCAACAAGTGCATTCAGCGACTAAGAAAGATTTTTCATTCGGTTGGAGCTAGCAGCGAAAAATTTACCCCCTCAGCTGAAGACCTACCACAAACCTTCGAACACATTGAGGGGGAAATTGACGAGCTCGACGAAGTCATAGCTGGGCATGGTGATTTCTGTGCCTGGGTAGCTTCTCGAGGGACTGCTGCAGCCTTCATGAAGGCTGGCTGTGAACATGGAAAAGTTGTTAACAGACCCACCTTCGCCTTATCTCCATCAATCCTGGATGATATGCCTGACCTTGCCCGAAGTATCTCCAACAGATTTATAAAAATGATATGGACAAAAGGCGGGCGGGAGAAGGCTGGAGATGAAGCACGAAGCCATCTTGAACCAGTAAGAGATAATACTTCGTACTTACCTTTTTCTTTGCACTTGATTTTTACTCACGGTTCCTTGATTTATGTAGGATGACGAAGGTGAAGATGATGCCTAAATTATGTCGTCGAAGCTGAAACTTAATGAAGATCAGTAGAAGTGTACTGTAGGAAAACTCAGGATATTTTTGTAACAATCCTTGTAAATACAACTAGACTATCTTCAAGGAACTTTGTACATACCTTGCAATGTATTCTTACCCTCTGCTTGAAGCGCTTTGATGTGGACGAAACCAGTATTTTGAGCCGAAGGCGAAAAACACCTTCCCTTCTTTTCGTACACAACGAAGCTTTAAAAGGTCGCTTCCTCTTTTTGCCGAAGCTTTGCTTTTTTGTACATGAAAACTACTTCTCCTTTCTGCCGAAGCTTTTCTTTACAAAACATAAAAAACTACTTCTCTTTTCTGCCGAAGCTTTCCTTTACATGACAAAACATAAAAGACTACTACTCTTTTGCACAACGATTCGTAAAAATCCAGTTCTCCCTTATACTGAACTTTTCCTTGTGCCAAAGCAACGGAACTTTTCACTTTTGCACACAACATAGCGTAATAAGTCATAAAAGGTACTTCTCCGAAGCTTTTTTGCCGAAGCAGCCACTTGGGAACACAAATGCTATGAATGAATGCTTATGCATGCGAATGTTATGATGTAATGTAATGCACGAATGAATGTCCGAAGCATATGTCCGAAGCCATATTGTCAGCCATTACTTGAAAACAACCACACATTAGCTCTGCATTCCCTTAGGAACGACTTTGGAGCTTCTTCGCCTCTTACTTAGGCAATATCAGCGTTGACTTTTCGCTGTAAGCTCTGCATCCCCTTAGGGACGTCTTTGGAGCTTCTTCGTCTTTTACTTAGACGGTATAAGCTCTGCATTCCCTTGGGAACGTCTTTGGAGCTTCTTCGTCTTTTACTTAGACGGTATAAACTCTGCATTCCCTTAGGAACGTCTTTGGAGTTTCTTCGCCTTTTACTTAGGCGGTATAAGCTCTGCATTCCCTTGGGAACGTCTTTGGAGCTTCTTCTCTTTTTTCTTTTTCAGTTTCTGCACTCGATGGTGCGTTCTCAGCTGTTACATTTACATTTTTTGGGGGATTTCGCTCTTATAAGACTAAAAAAGGAAATTACACATGATGGCCCTATTAAAAACCTTTCTCCCCCTTCGGAAAGGAAAAGGGTGCCATGAAAATGAAAAGAAAAAGCATAAAAAATTACATCATATTATACATAGTATCGCCGAAGCTCATCCGCATTCCAAGACCTTGGAATTTCGTTGCCATCCATGTCCTTCAATCTGTATGATCCAGGCCTTGACGAAGATACTACTAAGAATGGTCCTTCCCATTTCAACTGTAGCTTACCCACTGTATCTGGGTTAGCCACTCTCCGAAGCACCAAGTGTCCCGGCTCAATATTTTTTAGCCGGACTTTTCTATCTCGCCATTTGACTGTTTCAGCCTGATATTTATTAATATTCTCCACGGCCTGAAGCCTGATCCCCTCTAAAGCATCTTTTTCCACAAGATAAGCATCTTCGGGGCCTGATTCTGCCGAAGCTACTACTCTTACTGACCCAGCTTTTGCTTCCTCCGGAGTTATTGCTTCGTCACCGAATAATAATTTGAATGGGGTAAAGCCTGTAGACCTTGATGTTGTTGTATTGTGGCTCCACACCACTTTGATTAACTGATCTGGCCACTTTCCCCTGGGTTGATTGAAGATTAACTTCATTATTCCTGTCATTATAATGCCGTTGGCCCTTTCAACGAGCCCATTTGACTCCGGATGCCTGACTGACGCAAAATGGATCTTCGTTCCGATTTGATTACAGAAGTCTCTGAAAGCTTCGGAGTCAAACTGCGTTCCATTATCTACAGTAATTGCCTTCGGTACCCCGAAGCGACAGACAATATTCTGCCAGAAAAACTTTTGGACAGTGGCTGAAGTTATTGTGGCCAATGGCTTCGCCTCAATCCACTTGGAAAAATACTCCACAGCCACTATAACATATTTTAGATTCCCTTGAGCCGGTGGTAATGGGCCCAACAAGTCAAGGCCCCACCTTTGCAATGGCCAGATGGGTTGTATCAGCTGTGTTAAAGACGAAGGTTGTTTTTGATCTCTTGCACATTTCTGACAACCTTCGCACTTTTGCACTAACTCCGCTGCATCCGAAGCTGCCTTCGGCCAATAAAATCCTTGGCGGAAGACTTTCCCAAGTAATGGCCTAGATCCAATGTGGGATCCACACAGGCCTGCATGTATCTCTTTCATCAACTCTATACCTTCGGCTCTAGATAAGCACTTGAGCAGCGGAGCACAAACTCCATGTTTGTATAATTCCCCTTCTATCATGACATACGGACGAGCTCTTGCCTCTATTCTTTTATTGTAAGCTTCGTCATCTGAAAGGGACTTACCCTGAAGGTAAGAGATTATTTCAGTTCTCCAATCTTCGCTGTAAACAGGAGATATGTTGAGGACTGCTCTTTCAAGGAGCTCCACTGAAGGTGCCTTTATTGTTTCGAAAAACACATCCGAGGGTAACGGCAGCCCCTGTGCCGCAGACTTAGCTAGCAAATCAGCATGCTCATTTTGTCCTCGAGGAATATTCTTGACCGAGAATCCTTCGAAGGATGCCTCGATCCTTCGGACCGTATCTAGATACTTTTCAAGCTTCGGATCTTTAGCTTTGCAACTTTTGTCAACATGACCCGAAACCACCTGGGAATCAGTTTTAAGAATTGCCCTTCTGATTCCCATTGCCTTTAATTTCCGAAGGCCCAAAAGCAGGGCTTCGTACTCAGCAATATTGTTCGTGCAGCTGAAATCAAGTCTTGCTGCGTAACAAGTTTTGACATTGGATGGTGAAACCAACACAGCAGCTGCACCTGCTCCGAAGATTCCCCAAGAGCCATCACAAAACACTGTCCACACTTCGGCATCTTTATTTGCTTCTTCATCCTTCGCCCCTGGTGTCCAGTCGGCAATGAAATCTGCCAATGCTTGAGACTGGATCGAAGATCTATGCACATAATCAATGTAAAATTCGTTGAGCTCTGCAGCCCATTTCCCAATCCGTCCAGTAGCTTCTCTATTTCTCATTATATCCTTCAACGGCTGCGAAGAAGGAACAATGATATTGTATGCCTGAAAATAATGCCGAAGCTTCCTGGATGCCATTAAAACGGCATATAATACCTTCTCCAGCTCTGTATAATTTTTCTTTGAGACACTAAGGACCTCAGATACAAAGTACACTGGAACTTGCTTCTTAAGCTGGCCATAAAGCTTCTCCTGGACAAGCGCCGCACTTACTGCTGAGTGCGAAGCTGCCACATATAACAACAGAGGAGCCCCTGGCGTTGGCGGAGTTAATGTTGTGAGATCTATCAAGTATTGCTTCAACTCTTCGAAGGCTTTTTGTTGACTTGGGCCCCATTGAAAGACTTCGGCTGACTTCAGCACCTCGAAGAATGGTAAGTTTCTTTCTGCTGATCTGGATATAAATCTGTTGAGAGATGCTAGCCTTCCTGTCAATCTTTGGGCCCCTTTTCTTGTAGTTGGTGGCTCCATTCGAAGTATAGCTTCGATTTTATTTGGATTAGCTTCGATTCCCTTTGTTGAAACTAAGCATCCAAGAAATTTACCCTTCTTTACTCCGAAGACACATTTCTCTGGATTCAGCTTCAGACCAGCTTGTCTGAAGCTGGCGAAGGTCTCCTGCAGATCAGCAATATGGTCCTCTTGCTTCGTGCTTTTGACGATAATGTCATCAACATAGGTCAACACATTTCTACCTATTTGAGACTGGAGAACCTTCGCAGTCATTCTGCTGAAACTTCCTCCAGCGTTTTTGAGCCCCTCAGGCATCCGAAGATAGCAATACGTGCCACTTGGAGTTATGAAGCTAGTTTTCGGCTCATCTTCCTTTTTCATCCAGATTTGATGATATCCTGAGTAACAGTCCAAGAGACTCATGAGCTCTGAAGAAGCTGCTGCATCGACTAGAGAGTCTATCCTTGGCAACGGGAATTCGTCCTTCGGACAAGCTTTGTTGAGATCTGTGAAATCGATACACATTCTCCACTTGCCATTGGCCTTCTTCACCATAACAGTGTTAGCTAGCCACTCTGGGTACTTCACTTCTCTGATAACTCCTGCACTGAGGAGTCTTTTTACTTCGTTGCGAGCCCCTTCGGCCTTGTCATCAGACATTTTCCGAAGCCTCTGCTTTCGGGGTCTAAAGGATGGGTCAACATTGAGCGAATGTTCAATAACATCCCGGTTTACTCCACAGAGATCATTAGCCGACCATGCAAAAACATCTTTGTTGTTGAATAAAAACCTTATCAAGGTTTTCTCCTGGTCTTCAGATAACTGCGAGCCCAACAGCACCTTCTGATCTGCTATGTCTTCGCACAATAGCATGGGCTTCGGCTGATCAGCCGAAGCTGCTTTTTCCCTCCTGAACTTGTACTGTTCACAAGCTTCAACTCCATCTATATTATGGATTGCCTTGGAATCAGTCCAGCTTCCTTCGGCCCTTCTGGCAGCTTCCTGACTCCCATGAATAGCAATAGGCCCTTGGTCCGAAGGTATCTTCATGCAGAGATAAGCTGGGTGAAGAATTGCTTCAAAAGCATTTAGGGTACCACGACCAATGATGGCGTTGTAGGGGTATTCCATGTCAACAATATCAAACACAATTTGCTCAGTCCTTGTGTTATTAACAAATCCGAAGGTTACCGGCATGGTAATCTTCCCGAGTGCCACAATCTGTCGCCCTCCGAAGCCACAAAGAGGGTGCGTAGCATCATGAATCTTGTCTTCAGGCTCTTGCATCTGTCTGAAGGCTTTGGCAAATATGATGTCAGCTGCACTGCCTGTGTCGACCAAGACATTGTGGACCAGAAATCCTTTGATAACACAAGAGATAACCATGGCATCATTGTGTGGGTAATCTTTAAGCTGAAGGTCCTCTTGGGAGAAGGTAATTGGAATGTGAGACCATTTTGACTTAATGAAGGGTCCCTGCACGCCAACATGCTGCACCCTTCTCTGAGCCTCCTTCTTCTGCCTTTTGTTAGCTGGCTCTGAGCAAGAACCGCCTGTTATCGGGAGCACCAGCTTCGAAGCCGAAGCAGCTCCAGCTTGAGTGTTGAACGAAGCCATCAGCTCAGAAAGGTGGAAGTGAGTTGACCGGAGGTGGGCGCCAATGTTGGGGACTTGTTCTCAAATGCT	.	PASS	ChrB=chr2;DupType=copyloss;END=11964;EndB=71754416;StartB=71745602;VarType=SR

My vcf after combine:

##fileformat=VCFv4.2
##contig=<ID=chr2,length=244442276>
##INFO=<ID=ACO,Number=A,Type=String,Description="Allele call-set origin(s) (<call-set>:...)">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr2	3106	.	C	CTTCGGTCCTGCGGAAGGCAAAGGTACAAGCGTGATGCGAAAGCAAATGACAGGTTCACGTGAACAGTACAGAGGTACTGTTCATCTATTTATAGGCACAGGTCGCAGCCTGTGACAAATTACAATTATGCCCCTTGCGAAAGTTTATAGCATTAACTCAGACTCATATGTATAAAAAGGTCATTCTATCTCTATGTCGGTTTAAAAACGCCGAAGCTCCATGAAAAGGGACCTTCGGCCATCTCTTGGAGACGACTTCAGCCGAAGCTGCTTCTTCATGTGAGACCTTCGGCGCACCGAAGCACGACCCCAACAGTAGCCCCTTTCGCGGTGCTAGATCGTTCTTCGTAACGAGCTTGACCCGTGAAAAAAGCCTCTTCAGCTTCGGGAAGCCGAAGGTCCAAAAAACACCTTCCCTGAGCTCGTTGCGGAGAAACGATCCGACTTCCGAGCGCGTGTCGGTCCCACCTTGCAGAGTTACTGTTTGATCCTTGCGGTCCACTGCGCAGCGGGTACAAGTTACGGCGCGCCTGGTGTAACAATTCCGCCGCTTCGCCTTGTTTCCTGCAGTACTATATAAACAAGCAGGTAGGTGTAAAGTTACCACAGCATTCATTGCTATTTGCACTGTTTTGCTGCCGAAATTTTCCATCATAGCCGAAGCTTAAATCCCAAAATCGAACGAAGGTCCGTCTCGACACTTGCTTCGTCAGAAAGAAGAGCTTCGGAGAGAAGAAAAAAGTAAAAAGTTTCTGACTTCCCAAACTTAAAATCAAATGGCGAGAATTCGATCTACTGCCAAAGTTGTACGCGAGGGAGACGAAGCCGAAGGTTCAAACACTGTGCCCATCTCCGAAGCGATGCAGCGCTCCGGTCTAGTGGCTGCGGAAGAGAGGCCTGGTACCGAAGCAAACCCGACAACAGCCGAAGAAGAAAACATTGATGGGACTGACTCCGGAGATGACTACCACATGTCTACACCCAGCAAGCCCAGTCACCTGGATTTTGGAAAATCAACTGTTTCAAAGGCTGACCTTGCGAAGATGATAAAGGCAGGTTTTTTCAAAGAAGATCAAAAAAAGCTACTTCGCTTCGGAGGAGAGGAGACTACCCCGAAGCCAGAGAAGGATGAGATTGTAATTTTCAAAAGCTTTTTAAAAGCTGGGCTGAGATTTCCTCTTCATGGAATTATTGGAGATGTGTTGCAAAAGTTTGGCATTTATTTTCACCAATTGACTCCTAACGCCATTGTTAGGCTTAATGTTTATATTTGGGCTCTCCGAAGCCAAGCTGTGGAACCGTTTGCCGACAGCTTCTGCCGAGCGCACGAATTACATTACCAAACGAAGGCCAGAGCAGACGGACTACATGATAATTTCGGCTGTTACAATTTTGCCTACCGGAAGACAACAAAGTGTCCTGTTATCAGCTACCGGAGCAAATGGCCAGCAGGCTGGAAGTCTGAGTGGTTCTACGTAAAAGTTGACGAAGACAGAGAAAAATTGATACAAAGTCCTCTGGAATTAATCTTCGGAGAGACAAGGCCACACTGCCACATCGGCGATTTAAAGGGTCCTACCTGGGCCGCTCTGGGTGAATTCGAAATTATTTCAGAACATATTGGCACCAGGGATCTGGTTCAGGAATTTTTGGCATTCAGAGTTTTCCCTACTTTAAAAGAGTGGGAGATGCCGAAGCTGGAGGGAGAGAAGAAGGAGGGGGAGCTTGTTCGTCTGCCTTATCACTTTAAATTCAAGAAGTACTTTAAGAAACCCTGCAAAGAGTGGTTGGACACAGTTGAGACAATGTGCAATGAAATCTTGGGGAACTACTCCAAAAAGGAGGATCAATTAATGACAGCAGCCTTCGGCACCCGACCGAAGCGAAGGCTGAACCGAGTATTCGATGCCCTGGGCTTCGAGTATCCAGACTATGAGCAGTTGAATAAGGGTGCCGAAGGCCACAAAAGAAAAAGAGTGACTGAAATTCTGACGAAGGATGAAGAGCAACCAGCAGCAGAGAAGAAAATTCCAAAGAAAAGGAAAATATCAACTCCGAAACGGAAAATATCCAAAGAAGAGAAAACCCCCACACCGCCTTCTACTAGCGACATAGAAGAAATTTTAAAGGTAATGACTGAACCCATGCCTACGAAGCTAAGTCCACTAGGGCTCCAACTGACGAAGCTTTTTCGAAAGGTGGACGAGCCGGATCAGACGAAGACAAGCAAACCCAAGCGGCAAAGAATCATTGCGGTAACTGAAGTTATCGATAAGACGCCGCCAAGGGCGTCAATCCAAAAAACGGCAGCTGCCGAAGGTGCAGCAATTGTCGAAGGCGTAGCTTCGGGGGTCGCGGCTACCGAAGCCGCTACAGCCGAAGATACAAACTTAAAAACCACGATTACGAATATCAACAAGATTTTGGAAGACATGGCCGCGGAAGAAACTGGTGCTACTTCTGAAAAAACCATGGCCACAGTGCCTGAAAAAGGAAAAGAAATAGCCGAAGACCCTTCGGATGACGAAGCATACACTTTCCAGAACTTAGTTGGGCAAAAACTGACGAAGGAGGAAATAGAAGAACTTAAAGAATACGCCAAGTCTTGCGGGTACAAGTCAGGTGCCCTCCTATTTGGGGGTGTAGATGATGAACAACTGGGCTGCATCCGGGACTCAGCTGGGGCTAAGGTCATCGGTACTTTATCAAAGAGTATCGGTTTTCCGAAGCTGGAGTCAGACATCAGCCGCTACCGACGACAACATGTCGTTGGTAGTTTATTTTATTCTAACTTCAAGGTGAATGACTTGTTTCTTAACCTTTATTGCTTCTAATAAAAACATGACTGACGAAGGTTGTGTTTGTGTAGAGTATGCTATTGAGCAAGGCTTTGCAAATGCAGCAGGATCTTGAAGATAAAAAGCATGAAGTTATAATTGAAAATTTGGAAAACAAAATAAAGGAACAATCAGATGCTTTTGAGAAAAAGAGCTTCGAACTCCAGGCAGCCGAAGGTTTACTGGCGGAAGCTGAAGCAAAAATATTAGAACTGAACACGAAGCTTCTCCGCCAGTCTGAGCAGTTCGAACAAGAAAAACAAGATCTCAATGCAAAACTTGAAGCCGAAGCTCAGCAAAATTCGGATTTGAGAAAATTATTGACAAATCTTCAAGAAAAATGCCTAGAATTTAGCAACAAGTGCATTCAGCGACTAAGAAAGATTTTTCATTCGGTTGGAGCTAGCAGCGAAAAATTTACCCCCTCAGCTGAAGACCTACCACAAACCTTCGAACACATTGAGGGGGAAATTGACGAGCTCGACGAAGTCATAGCTGGGCATGGTGATTTCTGTGCCTGGGTAGCTTCTCGAGGGACTGCTGCAGCCTTCATGAAGGCTGGCTGTGAACATGGAAAAGTTGTTAACAGACCCACCTTCGCCTTATCTCCATCAATCCTGGATGATATGCCTGACCTTGCCCGAAGTATCTCCAACAGATTTATAAAAATGATATGGACAAAAGGCGGGCGGGAGAAGGCTGGAGATGAAGCACGAAGCCATCTTGAACCAGTAAGAGATAATACTTCGTACTTACCTTTTTCTTTGCACTTGATTTTTACTCACGGTTCCTTGATTTATGTAGGATGACGAAGGTGAAGATGATGCCTAAATTATGTCGTCGAAGCTGAAACTTAATGAAGATCAGTAGAAGTGTACTGTAGGAAAACTCAGGATATTTTTGTAACAATCCTTGTAAATACAACTAGACTATCTTCAAGGAACTTTGTACATACCTTGCAATGTATTCTTACCCTCTGCTTGAAGCGCTTTGATGTGGACGAAACCAGTATTTTGAGCCGAAGGCGAAAAACACCTTCCCTTCTTTTCGTACACAACGAAGCTTTAAAAGGTCGCTTCCTCTTTTTGCCGAAGCTTTGCTTTTTTGTACATGAAAACTACTTCTCCTTTCTGCCGAAGCTTTTCTTTACAAAACATAAAAAACTACTTCTCTTTTCTGCCGAAGCTTTCCTTTACATGACAAAACATAAAAGACTACTACTCTTTTGCACAACGATTCGTAAAAATCCAGTTCTCCCTTATACTGAACTTTTCCTTGTGCCAAAGCAACGGAACTTTTCACTTTTGCACACAACATAGCGTAATAAGTCATAAAAGGTACTTCTCCGAAGCTTTTTTGCCGAAGCAGCCACTTGGGAACACAAATGCTATGAATGAATGCTTATGCATGCGAATGTTATGATGTAATGTAATGCACGAATGAATGTCCGAAGCATATGTCCGAAGCCATATTGTCAGCCATTACTTGAAAACAACCACACATTAGCTCTGCATTCCCTTAGGAACGACTTTGGAGCTTCTTCGCCTCTTACTTAGGCAATATCAGCGTTGACTTTTCGCTGTAAGCTCTGCATCCCCTTAGGGACGTCTTTGGAGCTTCTTCGTCTTTTACTTAGACGGTATAAGCTCTGCATTCCCTTGGGAACGTCTTTGGAGCTTCTTCGTCTTTTACTTAGACGGTATAAACTCTGCATTCCCTTAGGAACGTCTTTGGAGTTTCTTCGCCTTTTACTTAGGCGGTATAAGCTCTGCATTCCCTTGGGAACGTCTTTGGAGCTTCTTCTCTTTTTTCTTTTTCAGTTTCTGCACTCGATGGTGCGTTCTCAGCTGTTACATTTACATTTTTTGGGGGATTTCGCTCTTATAAGACTAAAAAAGGAAATTACACATGATGGCCCTATTAAAAACCTTTCTCCCCCTTCGGAAAGGAAAAGGGTGCCATGAAAATGAAAAGAAAAAGCATAAAAAATTACATCATATTATACATAGTATCGCCGAAGCTCATCCGCATTCCAAGACCTTGGAATTTCGTTGCCATCCATGTCCTTCAATCTGTATGATCCAGGCCTTGACGAAGATACTACTAAGAATGGTCCTTCCCATTTCAACTGTAGCTTACCCACTGTATCTGGGTTAGCCACTCTCCGAAGCACCAAGTGTCCCGGCTCAATATTTTTTAGCCGGACTTTTCTATCTCGCCATTTGACTGTTTCAGCCTGATATTTATTAATATTCTCCACGGCCTGAAGCCTGATCCCCTCTAAAGCATCTTTTTCCACAAGATAAGCATCTTCGGGGCCTGATTCTGCCGAAGCTACTACTCTTACTGACCCAGCTTTTGCTTCCTCCGGAGTTATTGCTTCGTCACCGAATAATAATTTGAATGGGGTAAAGCCTGTAGACCTTGATGTTGTTGTATTGTGGCTCCACACCACTTTGATTAACTGATCTGGCCACTTTCCCCTGGGTTGATTGAAGATTAACTTCATTATTCCTGTCATTATAATGCCGTTGGCCCTTTCAACGAGCCCATTTGACTCCGGATGCCTGACTGACGCAAAATGGATCTTCGTTCCGATTTGATTACAGAAGTCTCTGAAAGCTTCGGAGTCAAACTGCGTTCCATTATCTACAGTAATTGCCTTCGGTACCCCGAAGCGACAGACAATATTCTGCCAGAAAAACTTTTGGACAGTGGCTGAAGTTATTGTGGCCAATGGCTTCGCCTCAATCCACTTGGAAAAATACTCCACAGCCACTATAACATATTTTAGATTCCCTTGAGCCGGTGGTAATGGGCCCAACAAGTCAAGGCCCCACCTTTGCAATGGCCAGATGGGTTGTATCAGCTGTGTTAAAGACGAAGGTTGTTTTTGATCTCTTGCACATTTCTGACAACCTTCGCACTTTTGCACTAACTCCGCTGCATCCGAAGCTGCCTTCGGCCAATAAAATCCTTGGCGGAAGACTTTCCCAAGTAATGGCCTAGATCCAATGTGGGATCCACACAGGCCTGCATGTATCTCTTTCATCAACTCTATACCTTCGGCTCTAGATAAGCACTTGAGCAGCGGAGCACAAACTCCATGTTTGTATAATTCCCCTTCTATCATGACATACGGACGAGCTCTTGCCTCTATTCTTTTATTGTAAGCTTCGTCATCTGAAAGGGACTTACCCTGAAGGTAAGAGATTATTTCAGTTCTCCAATCTTCGCTGTAAACAGGAGATATGTTGAGGACTGCTCTTTCAAGGAGCTCCACTGAAGGTGCCTTTATTGTTTCGAAAAACACATCCGAGGGTAACGGCAGCCCCTGTGCCGCAGACTTAGCTAGCAAATCAGCATGCTCATTTTGTCCTCGAGGAATATTCTTGACCGAGAATCCTTCGAAGGATGCCTCGATCCTTCGGACCGTATCTAGATACTTTTCAAGCTTCGGATCTTTAGCTTTGCAACTTTTGTCAACATGACCCGAAACCACCTGGGAATCAGTTTTAAGAATTGCCCTTCTGATTCCCATTGCCTTTAATTTCCGAAGGCCCAAAAGCAGGGCTTCGTACTCAGCAATATTGTTCGTGCAGCTGAAATCAAGTCTTGCTGCGTAACAAGTTTTGACATTGGATGGTGAAACCAACACAGCAGCTGCACCTGCTCCGAAGATTCCCCAAGAGCCATCACAAAACACTGTCCACACTTCGGCATCTTTATTTGCTTCTTCATCCTTCGCCCCTGGTGTCCAGTCGGCAATGAAATCTGCCAATGCTTGAGACTGGATCGAAGATCTATGCACATAATCAATGTAAAATTCGTTGAGCTCTGCAGCCCATTTCCCAATCCGTCCAGTAGCTTCTCTATTTCTCATTATATCCTTCAACGGCTGCGAAGAAGGAACAATGATATTGTATGCCTGAAAATAATGCCGAAGCTTCCTGGATGCCATTAAAACGGCATATAATACCTTCTCCAGCTCTGTATAATTTTTCTTTGAGACACTAAGGACCTCAGATACAAAGTACACTGGAACTTGCTTCTTAAGCTGGCCATAAAGCTTCTCCTGGACAAGCGCCGCACTTACTGCTGAGTGCGAAGCTGCCACATATAACAACAGAGGAGCCCCTGGCGTTGGCGGAGTTAATGTTGTGAGATCTATCAAGTATTGCTTCAACTCTTCGAAGGCTTTTTGTTGACTTGGGCCCCATTGAAAGACTTCGGCTGACTTCAGCACCTCGAAGAATGGTAAGTTTCTTTCTGCTGATCTGGATATAAATCTGTTGAGAGATGCTAGCCTTCCTGTCAATCTTTGGGCCCCTTTTCTTGTAGTTGGTGGCTCCATTCGAAGTATAGCTTCGATTTTATTTGGATTAGCTTCGATTCCCTTTGTTGAAACTAAGCATCCAAGAAATTTACCCTTCTTTACTCCGAAGACACATTTCTCTGGATTCAGCTTCAGACCAGCTTGTCTGAAGCTGGCGAAGGTCTCCTGCAGATCAGCAATATGGTCCTCTTGCTTCGTGCTTTTGACGATAATGTCATCAACATAGGTCAACACATTTCTACCTATTTGAGACTGGAGAACCTTCGCAGTCATTCTGCTGAAACTTCCTCCAGCGTTTTTGAGCCCCTCAGGCATCCGAAGATAGCAATACGTGCCACTTGGAGTTATGAAGCTAGTTTTCGGCTCATCTTCCTTTTTCATCCAGATTTGATGATATCCTGAGTAACAGTCCAAGAGACTCATGAGCTCTGAAGAAGCTGCTGCATCGACTAGAGAGTCTATCCTTGGCAACGGGAATTCGTCCTTCGGACAAGCTTTGTTGAGATCTGTGAAATCGATACACATTCTCCACTTGCCATTGGCCTTCTTCACCATAACAGTGTTAGCTAGCCACTCTGGGTACTTCACTTCTCTGATAACTCCTGCACTGAGGAGTCTTTTTACTTCGTTGCGAGCCCCTTCGGCCTTGTCATCAGACATTTTCCGAAGCCTCTGCTTTCGGGGTCTAAAGGATGGGTCAACATTGAGCGAATGTTCAATAACATCCCGGTTTACTCCACAGAGATCATTAGCCGACCATGCAAAAACATCTTTGTTGTTGAATAAAAACCTTATCAAGGTTTTCTCCTGGTCTTCAGATAACTGCGAGCCCAACAGCACCTTCTGATCTGCTATGTCTTCGCACAATAGCATGGGCTTCGGCTGATCAGCCGAAGCTGCTTTTTCCCTCCTGAACTTGTACTGTTCACAAGCTTCAACTCCATCTATATTATGGATTGCCTTGGAATCAGTCCAGCTTCCTTCGGCCCTTCTGGCAGCTTCCTGACTCCCATGAATAGCAATAGGCCCTTGGTCCGAAGGTATCTTCATGCAGAGATAAGCTGGGTGAAGAATTGCTTCAAAAGCATTTAGGGTACCACGACCAATGATGGCGTTGTAGGGGTATTCCATGTCAACAATATCAAACACAATTTGCTCAGTCCTTGTGTTATTAACAAATCCGAAGGTTACCGGCATGGTAATCTTCCCGAGTGCCACAATCTGTCGCCCTCCGAAGCCACAAAGAGGGTGCGTAGCATCATGAATCTTGTCTTCAGGCTCTTGCATCTGTCTGAAGGCTTTGGCAAATATGATGTCAGCTGCACTGCCTGTGTCGACCAAGACATTGTGGACCAGAAATCCTTTGATAACACAAGAGATAACCATGGCATCATTGTGTGGGTAATCTTTAAGCTGAAGGTCCTCTTGGGAGAAGGTAATTGGAATGTGAGACCATTTTGACTTAATGAAGGGTCCCTGCACGCCAACATGCTGCACCCTTCTCTGAGCCTCCTTCTTCTGCCTTTTGTTAGCTGGCTCTGAGCAAGAACCGCCTGTTATCGGGAGCACCAGCTTCGAAGCCGAAGCAGCTCCAGCTTGAGTGTTGAACGAAGCCATCAGCTCAGAAAGGTGGAAGTGAGTTGACCGGAGGTGGGCGCCAATGTTGGGGACTTGTTCTCAAATGCT	.	.	ACO=SIRY

[jonassibbesen]

I see why this is happening now. This is actually not a bug. Basically, combine will trim all right-side bases that are the same between REF and ALT. The variant itself is still the same, but it is now simpler and less redundant. Here is a example:

chr1 1 . CAC CACAC

after combine:

chr1 1 . C CAC

Here AC is trimmed from both the REF and ALT allele.

[zhiyongli1995]

Alright, thanks vary much for your reply, you solved my question.