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167 Open 1,119 Closed
167 Open 1,119 Closed
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Issues list

samtools reheader error
#2157 opened Dec 5, 2024 by C-YONG
2
how to get the mismatch rate for indel by samtools
#2152 opened Nov 26, 2024 by litun-fkby
2
Ambiguous Wording in Documentation
#2149 opened Nov 21, 2024 by DarioS
1
Coverage Threshold Must Be A Single Integer
#2148 opened Nov 21, 2024 by DarioS
@daviesrob
3
Is the order of the mpileup read bases (column 5) important?
#2146 opened Nov 20, 2024 by anderspitman
4
samtools merge single file too slow.
#2145 opened Nov 20, 2024 by y9c wishlist
"samtools view" regions have duplicate lines on the edges. Could them be limited by positions?
#2144 opened Nov 19, 2024 by lishengting
@jkbonfield
7
samtools stats reference information
#2139 opened Nov 6, 2024 by fgvieira wishlist
1
Samtools stats seems to incorrectly report inward/outward oriented pairs?
#2137 opened Nov 1, 2024 by rachaelanndetar
@vasudeva8
1
Suggest: add warning when filename extension and file content mismatch
#2094 opened Aug 6, 2024 by richelbilderbeek
@daviesrob
1
De-duplicate large sam file
#2091 opened Aug 2, 2024 by morien
@whitwham
3
Reimplement samtools stats
#1997 opened Feb 22, 2024 by jkbonfield
2
--output parameter for calmd and other commands
#1983 opened Feb 2, 2024 by y9c
1
Markdup on paired reads using --barcode-tag malfunctions if tag isn't present in both reads
#1978 opened Jan 29, 2024 by eboyden
@whitwham
Any way to skip fasta md5 check when generating CRAM file from BAM/SAM?
#1938 opened Nov 13, 2023 by karlestira
@jkbonfield
1
Bit for bit recovery of original fastq files
#1928 opened Oct 19, 2023 by hallundbaek wishlist
2
samtools query (similar to bcftools query): Write user defined output from BAM files or write calculated expressions to tags
#1897 opened Aug 3, 2023 by ghuls
1
Environment-dependent samtools view error (invalid BGZF header) with remote GCS BAM
#1811 opened Mar 16, 2023 by rlorigro
@daviesrob
8
barcode hash conflict?
#1741 opened Oct 28, 2022 by wulj2
3
Extended markdup UMI support
#1710 opened Aug 31, 2022 by Poshi
19
customized output for samtools coverage specifying the columns of interest
#1664 opened Jun 15, 2022 by nicolo-tellini
@whitwham
1
samtools coverage for WES using bed file
#1662 opened May 30, 2022 by amyhouseman
@whitwham
11
samtools faidx fails to retrieve large scaffolds
#1660 opened May 26, 2022 by mcshane
@daviesrob
7
samtools 1.15 become very slow when I set maxcnt to 8,000,000
#1654 opened May 6, 2022 by ymcki
2
samtools view command error
#1622 opened Mar 24, 2022 by skatragadda-nygc
@whitwham
12
ProTip! no:milestone will show everything without a milestone.