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21 Open 10 Closed
21 Open 10 Closed
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Issues list

Same output for all regions
#34 opened Jul 13, 2023 by soumyarao86
No output for low-coverage bam files
#33 opened Jun 20, 2023 by Npaffen
locating pairs in CRAM stopped working in versions after 1.0.1
#32 opened Feb 28, 2023 by seru71
1
Swapping first and second mates when pair aligned to reverse strand
#31 opened Feb 22, 2021 by mikisvaz
Build failed
#30 opened Jan 13, 2021 by Fred-07
Realignment to new ref needs recalibration?
#29 opened Nov 9, 2020 by TnakaNY
Issue with build
#28 opened Sep 23, 2020 by caleblareau
6
common use case - properly paired mates only
#27 opened May 14, 2020 by benbfly
feature request - colorspace reversion
#25 opened Dec 15, 2019 by berntpopp
feature request - single ended nanopore reads
#24 opened Oct 10, 2019 by colindaven
[feature request?] unmapped with -L 0:0*-0 / skip some reads sorted bam
#23 opened Jul 25, 2019 by evolighting
-L chr1 runs but does not output anything
#21 opened May 30, 2019 by bwlang
1
Inappropriate call if not paired read
#18 opened Apr 23, 2019 by ziaursani
2
samtools view -bSu in pipe is now redundant
#17 opened Apr 20, 2019 by tseemann
1
Reference MD5 mismatch for slice 2
#16 opened Apr 20, 2019 by YaCui
3
Missing Reads
#15 opened Mar 28, 2019 by christopher-schroeder
2
Compressed output
#14 opened Mar 7, 2019 by BrianLohman
1
remove reads that are mapped close each other
#12 opened Dec 25, 2018 by wsuplantpathology
2
Does it work for Bam files where sequences have been removed?
#11 opened Nov 27, 2018 by kvittingseerup
Get BAM or SAM output from tool?
#10 opened Oct 16, 2018 by cmdcolin
1
OutOfMemoryError
#9 opened Oct 10, 2018 by brentp
2
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