The target SV in *.svaba.sv.vcf is not found in *.alignments.txt.gz

[hhd1008611]

Hello,
By the code:
svaba run -t $TUM_BAM -t $NORM_BAM -p $CORES -k $k -a $name -G $REF
I found the target SV in *.svaba.sv.vcf, but the target SV is not found in *.alignments.txt.gz. Is there something wrong with my code? Please tell me if this is normal, thank you very much.

[walaj]

I can’t see the whole SV, but if is a discordant-read only SV (DSCRD), it won’t be in alignments (contigs) file.

…

On Mon, Jul 31, 2023 at 10:30 AM hhd1008611 ***@***.***> wrote: Hello, By the code: svaba run -t $TUM_BAM -t $NORM_BAM -p $CORES -k $k -a $name -G $REF I found the target SV in *.svaba.sv.vcf, but the target SV is not found in *.alignments.txt.gz. Is there something wrong with my code? Please tell me if this is normal, thank you very much. [image: image] <https://user-images.githubusercontent.com/35066896/257251221-f7206d3c-1fba-4b37-a690-f2437da5fcaf.png> — Reply to this email directly, view it on GitHub <#127>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUZ7CGMWL3IQPUMKQN42WDXS66RBANCNFSM6AAAAAA26LGAKY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[hhd1008611]

Tanks for you reply,
I checked the SV file according to what you said and found "EVDNC=DSCRD",
chr5 49456740 319614841:1 T ]chr5:49471796]T 29 PASS DISC_MAPQ=60;EVDNC=DSCRD;IMPRECISE;MAPQ=60;MATEID=319614841:2;MATENM=-1;NM=-1;NUMPARTS=0;SCTG=chr5:49456740(-)-chr5:49471796(+)__57_49455501_49480501D;SPAN=15056;SVTYPE=BND GT:AD:DP:GQ:PL:SR:DR:LR:LO 0 0 12 0/1:12:35:29.9:29.9,0,56.3:0:12:-29.78:30.29 0/0:0:25:6.9:0,6.9,75.9:0:0:7.024:0
so next I want to delete the discordant-reads and then run SVaba, because the discordant-reads do not affect CNV, which I also cited with IGV.

However, after deleting discordant-reads, *.svaba.sv.vcf found no SV, but there is clearly CNV from IGV. Something's wrong with my parameters or I don't have enough data?
Here's my code:

samtools view -b -f3 -@ 12 $TUM_BAM  > $TUM_BAM_dediscordant
svaba run -t $TUM_BAM_dediscordant -p $CORES -k $k -a $name -G $REF

[hhd1008611]

The order of the IGV diagram is:
first, $NORM_BAM
second, $TUM_BAM
third, $TUM_BAM_dediscordant

[walaj]

well the discordant reads are relevant for CNVs. What I think you mean is that they aren't substantial contributors to the copy-number. Svaba aims to compile rearrangement breakpoints, especially complex ones, that are most relevant in cancer genomes. For finding germline CNVs, you might try Lumpy