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169 Open 1,052 Closed
169 Open 1,052 Closed
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Issues list

[E::aux_parse] unrecognized type ':'
#2041 opened Apr 26, 2024 by chilampoon
2
ampliconclip retains sequence between two regions covered by the same read
#2040 opened Apr 24, 2024 by wiedenhoeft
Using view command to filter the records from bam file, but also report the number of reads passed the filter or dropped.
#2038 opened Apr 22, 2024 by y9c
Add a report of number of alignments for each primer to samtools ampliconclip
#2033 opened Apr 17, 2024 by bwlang
1
@whitwham
1
An error:[E::sam_hdr_create] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO
#2024 opened Apr 10, 2024 by shizuka0420
4
plot-bamstats: Issue with accuracy of quality score plot for Oxford nanopore long reads
#2017 opened Apr 1, 2024 by TBradley27
@jkbonfield
6
samtools reset SA-tag
#2011 opened Mar 25, 2024 by fellen31
1
@vasudeva8
Reimplement samtools stats
#1997 opened Feb 22, 2024 by jkbonfield
2
samtools fastq could merge pair members and output just a single FASTA/Q entry
#1991 opened Feb 15, 2024 by mmokrejs
@jkbonfield
1
--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
BAM Sequencing Integrity Hash
#1935 opened Nov 8, 2023 by hammad93 wishlist
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
samtools markup mark incompatible alignment(different CIGAR) as duplicates
#1788 opened Jan 28, 2023 by wulj2
2
barcode hash conflict?
#1741 opened Oct 28, 2022 by wulj2
3
Extended markdup UMI support
#1710 opened Aug 31, 2022 by Poshi
17
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
9
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
standardize I/O nomenclature across all tools?
#1569 opened Dec 22, 2021 by eboyden
17
ProTip! Exclude everything labeled bug with -label:bug.