Skip to content

Issues: samtools/samtools

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

168 Open 1,134 Closed
168 Open 1,134 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

samtools markdup: move UMI from read name to RX tag
#2181 opened Feb 4, 2025 by matthdsm wishlist
1
samtools sort: truncated file.
#2180 opened Feb 1, 2025 by GooLey1025
1
Samtools stats differ if the file is sorted by coordinate or queryname
#2177 opened Jan 27, 2025 by fgvieira
@daviesrob
1
The ability to stats a bam file for grouped genomic intervals at once.
#2172 opened Jan 18, 2025 by YuanfengZhang
@daviesrob
1
Samtools consensus --min-depth option produces longer sequence
#2167 opened Jan 14, 2025 by sanschiffre
@jkbonfield
4
samtools reheader error
#2157 opened Dec 5, 2024 by C-YONG wishlist
3
Coverage Threshold Must Be A Single Integer
#2148 opened Nov 21, 2024 by DarioS
@daviesrob
3
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
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
ProTip! Exclude everything labeled bug with -label:bug.