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samtools

7 indexed repositories · View on GitHub

samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data

C · 1956 stars
htslib
C library for high-throughput sequencing data formats

C · 950 stars
bcftools
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith...

C · 891 stars
hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats

TeX · 713 stars
htsjdk
A Java API for high-throughput sequencing data (HTS) formats.

Java · 303 stars
htscodecs
Custom compression for CRAM and others.

C · 40 stars
www.htslib.org
The http://www.htslib.org/ web site

HTML · 9 stars

Beginner friendly Everything

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[Bug]hts_getline() aborts on a bzip2-compressed input: hts_detect_format() classifies BZh-prefixed data as bzip2_compression, but the line reader only handles no_compression/gzip/bgzf and hits default: abort() (CWE-617) Open

Difficulty 3/5 1-2 days Newbie friendliness 74/100

samtools/htslib#2091 · Opened Sep 15, 2026
[Bug]Signed integer overflow in bcf_get_version() on the VCF header path: the version string ##fileformat=VCFv4.<huge> drives ver += tmp * 1000 past LONG_MAX (UBSan trap @ vcf.c:186, CWE-190) Open

Difficulty 3/5 1-2 days Newbie friendliness 76/100

samtools/htslib#2088 · 2 comments · Opened Sep 15, 2026
Add option to remove @SQ references when filtering to a target region with samtools view Open

samtools/samtools#2383 · 1 comment · 1 assignee · Opened Sep 15, 2026
VCFv4.5/4.4 Specification Inaccuracy -- Genotype Fields [§1.6.2] Open

Difficulty 1/5 Under an hour Newbie friendliness 88/100

samtools/hts-specs#871 · 1 comment · Opened Sep 11, 2026
VCFv4.5 Specification Typo -- Tandem Repeats [§5.7] Open

Difficulty 1/5 1-3 hours Newbie friendliness 92/100

samtools/hts-specs#870 · 1 comment · Opened Sep 11, 2026
VCFv4.5 Specification Inaccuracy -- Large Insertions (Circular) [§5.4.2] Open

Difficulty 1/5 Under an hour Newbie friendliness 88/100

samtools/hts-specs#869 · Opened Sep 11, 2026
Samtools markdup --move-umi-to-tag Open

samtools/samtools#2380 · 2 comments · 1 assignee · Opened Sep 9, 2026
stats: coverage distribution (COV, -t/-g target percentage) wraps around a fixed ring buffer for spliced alignments and drops counts on buffer reallocation Open

Difficulty 4/5 3-5 days Newbie friendliness 68/100

samtools/samtools#2378 · Opened Sep 8, 2026
Examples using Number=P and/or PSL/PSO/PSQ fields Open

vcf

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

samtools/hts-specs#868 · Opened Sep 6, 2026
Add option to `samtools markdup` to not consider strand orientation Open

samtools/samtools#2377 · 3 comments · 1 reaction · 1 assignee · Opened Sep 4, 2026
mpileup + Varscan2 issue samtools 1.24 Open

samtools/samtools#2375 · 1 comment · 1 assignee · Opened Aug 31, 2026
samtools consensus uses so much memory it is unable to complete Open

samtools/samtools#2374 · 15 comments · 1 assignee · Opened Aug 28, 2026
cram: Clarify whether tag ID lists are separated or terminated Open

cram

Difficulty 2/5 1-3 hours Newbie friendliness 70/100

samtools/hts-specs#867 · Opened Aug 25, 2026
Allow http QUERY method in htsget Open

htsget

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

samtools/hts-specs#866 · Opened Aug 25, 2026
The meaning of an "optional field" VCF and a clash with ##contig Open

vcf

Difficulty 5/5 Over a week Newbie friendliness 45/100

samtools/hts-specs#865 · 2 comments · Opened Aug 13, 2026
Recommended practice "No alignments should be assigned mapping quality 255" is ambiguous Open

sam

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

samtools/hts-specs#864 · 2 comments · Opened Aug 11, 2026
Fix or ignore "Tag Type in wrong order" Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

samtools/htsjdk#1796 · Opened Aug 11, 2026
EVENTTYPE can be different for records with the same EVENT Open

vcf

Difficulty 3/5 1-2 days Newbie friendliness 45/100

samtools/hts-specs#863 · Opened Aug 10, 2026
[merge] fix primary alignment flag Open

samtools/samtools#2359 · 9 comments · 1 assignee · Opened Aug 5, 2026
SamPairUtil.setMateInformationOnSupplementalAlignment copies TLEN from the mate primary instead of computing it Open

Difficulty 2/5 Half a day Newbie friendliness 82/100

samtools/htsjdk#1795 · Opened Jul 31, 2026
Error in VCF test files Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

samtools/hts-specs#860 · Opened Jul 25, 2026
Samtools checksum changes output between 1.23.1 and 1.24 Open

samtools/samtools#2354 · 6 comments · 1 assignee · Opened Jul 24, 2026
No const qualifiers using htscodecs API. Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/htscodecs#151 · 3 comments · Opened Jul 6, 2026
Issue in gff2gff.py script - does not generate the output file Open

needs-feedback

Difficulty 3/5 1-2 days Newbie friendliness 55/100

samtools/bcftools#2572 · 1 comment · Opened Jun 25, 2026
rlen calculation in bcf/vcf Open

vcf

Difficulty 4/5 3-5 days Newbie friendliness 45/100

samtools/hts-specs#857 · Opened May 29, 2026
CI testing for signed-off-by commits Open

samtools/htslib#2014 · 1 assignee · Opened May 20, 2026
Add optional progress output for long-running subcommands (mpileup, view, norm, index) Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 45/100

samtools/bcftools#2559 · 3 comments · Opened May 16, 2026
Feature request : bcftools annotate and discordant chromosome notation Open

htslib-dependent P2: Desirable

Difficulty 3/5 1-2 days Newbie friendliness 48/100

samtools/bcftools#2549 · 1 comment · Opened May 7, 2026
Feature request: use pedigree information for SNP calling Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

samtools/bcftools#2546 · 2 comments · Opened Apr 28, 2026
bcftools merge fills missing fields with "^@" instead of "." Open

needs-feedback requires-test-case

Difficulty 3/5 1-2 days Newbie friendliness 55/100

samtools/bcftools#2539 · 2 comments · 1 reaction · Opened Apr 2, 2026
ITF-8/LTF-8 spec text has typos, an incorrect prefix description, and lacks examples Open

Difficulty 3/5 1-2 days Newbie friendliness 65/100

samtools/hts-specs#855 · 4 comments · Opened Mar 31, 2026
Diff / patch like program for efficient storage of raw + processed data Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

samtools/samtools#2318 · 2 reactions · Opened Mar 26, 2026
split-vep only prints first numerical value Open

requires-test-case

Difficulty 3/5 1-2 days Newbie friendliness 52/100

samtools/bcftools#2516 · 5 comments · Opened Mar 23, 2026
MIN_DP should be updated from DP not just other MIN_DP records. Production of a MIN_DP record when none are input. Open

requires-test-case

Difficulty 3/5 1-2 days Newbie friendliness 48/100

samtools/bcftools#2515 · 2 comments · Opened Mar 22, 2026
HTSJDK QUAL floating-point precision error from log10PError round-trip Open

bcf bug vcf

Difficulty 4/5 3-5 days Newbie friendliness 45/100

samtools/htsjdk#1757 · Opened Mar 20, 2026
bcftools mpileup for a set of Illumina+HiFi reads Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

samtools/bcftools#2511 · 4 comments · Opened Mar 12, 2026
feature request: polyploid variant calling Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

samtools/bcftools#2508 · 11 reactions · Opened Mar 2, 2026
bcftools annotate doesn't liftover fields from VCF with symbolic alleles if END in only one file. Open

requires-test-case

Difficulty 4/5 3-5 days Newbie friendliness 48/100

samtools/bcftools#2507 · 1 comment · Opened Mar 2, 2026
Suggestion: populate INFO name in warning "INFO tag id=146" Open

samtools/htslib#1996 · 4 comments · 1 assignee · Opened Feb 20, 2026
cannot specify single read for casava fastq import Open

samtools/samtools#2307 · 1 comment · 1 assignee · Opened Feb 14, 2026
Missing value for SVCLAIM in DEL/DUP in VCFv4.4: clarification and addition Open

vcf

Difficulty 4/5 3-5 days Newbie friendliness 30/100

samtools/hts-specs#849 · 1 comment · Opened Jan 19, 2026
Is the set of `##ALT` top-level types in IDs *really* restricted to the 5 provided? Open

vcf

Difficulty 3/5 1-2 days Newbie friendliness 35/100

samtools/hts-specs#848 · Opened Jan 15, 2026
samtools markdup memory usage on high-depth regions Open

samtools/samtools#2296 · 1 assignee · Opened Jan 15, 2026
how to index a read in a circular sequence? Open

sam

Difficulty 5/5 Over a week Newbie friendliness 25/100

samtools/hts-specs#847 · 1 comment · Opened Dec 18, 2025
Incorrect allele ("2") in... when trying to merge, merged files Open

requires-test-case

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/bcftools#2488 · 1 comment · Opened Dec 12, 2025
norm -m + --atomize inconsistent representation of complex variants Open

D1: Difficult P2: Desirable

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/bcftools#2482 · 1 comment · Opened Nov 24, 2025
A molecular-annotation-spec for SAM/BAM/CRAM with new reserved tags Open

sam sam-tags

Difficulty 5/5 Over a week Newbie friendliness 25/100

samtools/hts-specs#846 · 4 comments · Opened Nov 20, 2025
Incorrect error message for out of order SAM file alignments Open

bam bug sam

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

samtools/htsjdk#1750 · Opened Nov 17, 2025
bcftools csq throw sanity_check_ref error and could not pass by --force Open

requires-test-case

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/bcftools#2478 · 3 comments · Opened Nov 14, 2025
documentation for `--pair-logic` is missing Open

Difficulty 1/5 Under an hour Newbie friendliness 55/100

samtools/bcftools#2472 · 1 comment · Opened Oct 28, 2025

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