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173 Open 1,068 Closed
173 Open 1,068 Closed
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Issues list

Samtools Consensus Clarification for Heterozygous sites >1bp in length
#2069 opened Jun 7, 2024 by NicMAlexandre
plot-bamstats fails when only one RL is in the stats file
#2068 opened Jun 7, 2024 by mariyeta
1
Header loading time depends on header names
#2066 opened Jun 5, 2024 by hjruscheweyh
4
Progress monitor
#2065 opened Jun 3, 2024 by chaplin89
@whitwham
1
Windows build
#2064 opened Jun 3, 2024 by chaplin89
@jkbonfield
3
Error when piping in BAM data to samtools on Windows
#2061 opened May 27, 2024 by divonlan
@jkbonfield
3
samtools view with -L, -M and --fetch-pairs doing full CRAM traversal
#2059 opened May 23, 2024 by acorvelo
@daviesrob
2
samtools split on a select list of tags
#2058 opened May 22, 2024 by cathalgking
@daviesrob
1
bgzip'ed output from faidx
#2055 opened May 17, 2024 by fgvieira
1
@vasudeva8
Should qname affect mpileup reults?
#2046 opened May 4, 2024 by smlchen
@jkbonfield
6
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
@daviesrob
1
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
ProTip! no:milestone will show everything without a milestone.