samtools/bcftools

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This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

Stars: 891
Forks: 277
Open beginner issues: 0
Indexed issues: 331
Avg merge: 2d 23h
Merged PRs (30d): 2

Dominant language: C
License: No license data
Last GitHub push: Sep 10, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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331 open issues indexed

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
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
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
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
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
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
Feature Request: +setGT plugin ability to set GT in a subset of samples in the VCF file Open

documentation enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

samtools/bcftools#2467 · 5 comments · Opened Oct 13, 2025
[FEATURE REQUEST] Window limits for removing duplicates/normalizing Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

samtools/bcftools#2461 · 1 comment · Opened Sep 30, 2025
bcftools norm -m+snps not merging adjacents snps Open

D1: Difficult enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

samtools/bcftools#2460 · 3 comments · Opened Sep 30, 2025
--include "FIELD=@file" fails silently even when single-value filter works Open

enhancement

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

samtools/bcftools#2459 · 1 comment · Opened Sep 25, 2025
bcftools 1.20 view command seems use all available CPUs despite the --threads 1 argument Open

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

samtools/bcftools#2455 · 6 comments · Opened Sep 9, 2025
bcftools +prune behavior question: --AF-tag AF must be set for -N maxAF to work? Open

requires-test-case

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/bcftools#2449 · 1 comment · Opened Aug 13, 2025
Calculating variables from samples matching filtering expressions Open

documentation

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

samtools/bcftools#2444 · 1 comment · Opened Aug 6, 2025
SVLEN tag interfering with the comparison between FASTA and VCF REF by bcftools consensus Open

htslib-dependent

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

samtools/bcftools#2439 · 1 comment · Opened Jul 23, 2025
feature request: inverse of --atomize (bcftools norm -m +any does not join two overlapping variants) Open

D1: Difficult enhancement

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

samtools/bcftools#2438 · 1 comment · Opened Jul 21, 2025
Building sequences using ref+clinvar but there are no variant applied (no errors given) Open

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

samtools/bcftools#2433 · 3 comments · Opened Jul 9, 2025
bcftools view changes GT format field value when it is declared as Type=Integer Open

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

samtools/bcftools#2431 · 1 comment · Opened Jul 3, 2025
bcftools view to subset VCF by region file in BED format gives only header without warning or error Open

requires-test-case

Difficulty 1/5 Under an hour Newbie friendliness 25/100

samtools/bcftools#2421 · 1 comment · Opened Jun 19, 2025
Question about id mode and the flipping action Open

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

samtools/bcftools#2403 · 1 comment · Opened May 8, 2025
could not parse the input VCF Open

requires-test-case

Difficulty 3/5 1-2 days Newbie friendliness 25/100

samtools/bcftools#2397 · 8 comments · Opened Apr 29, 2025
Print a warning if -r/R/-t/-T sequences use different chr naming convention than the VCF header Open

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

samtools/bcftools#2396 · Opened Apr 20, 2025
bcftools norm convert non-ATGCN IUPAC to N however mpileup and call does not. Open

requires-test-case

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

samtools/bcftools#2393 · 4 comments · Opened Apr 15, 2025
norm normalizing reference ALT is not counted in stats or old-rec-tag Open

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

samtools/bcftools#2391 · Opened Apr 10, 2025
concordance with indels issue Open

needs-feedback

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/bcftools#2388 · 1 comment · Opened Mar 27, 2025
mendelian2 plugin Open

requires-test-case

Difficulty 3/5 1-2 days Newbie friendliness 38/100

samtools/bcftools#2379 · 1 comment · Opened Mar 11, 2025
"-nan" GP and genotype coding in males Open

requires-test-case

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

samtools/bcftools#2377 · 6 comments · Opened Mar 7, 2025
How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF? Open

needs-feedback

Difficulty 3/5 1-2 days Newbie friendliness 25/100

samtools/bcftools#2376 · 1 comment · Opened Mar 5, 2025
Using COUNT with bcftools filter across all samples Open

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

samtools/bcftools#2363 · 2 comments · Opened Feb 1, 2025
bcftools 1.21 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants, continuation of #2333 Open

bug enhancement

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

samtools/bcftools#2356 · 4 comments · Opened Jan 21, 2025
The genotypes do not reflect the allele coverage frequency Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/bcftools#2352 · Opened Jan 9, 2025
Problems defining ploidy with bcftools call Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

samtools/bcftools#2351 · 1 comment · Opened Jan 7, 2025
consensus `--missing` not compatible with gvcf blocks Open

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

samtools/bcftools#2350 · 4 comments · Opened Jan 7, 2025
2 lines of InDel in the same position ? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/bcftools#2347 · 2 comments · Opened Dec 24, 2024
feature request: duplicate merging and selecting Open

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

samtools/bcftools#2342 · 1 comment · Opened Dec 18, 2024
Merge speed has not been increased by '--threads' option ? Open

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

samtools/bcftools#2340 · 2 comments · Opened Dec 17, 2024
strange handling of SVs by bcftools norm --fasta-ref Open

requires-test-case

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/bcftools#2330 · 3 comments · Opened Dec 6, 2024
Different parameters on different chromosomes Open

needs-feedback

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

samtools/bcftools#2327 · 1 comment · Opened Dec 1, 2024
[Feature Request] Cannot sort using custom contig order Open

enhancement

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

samtools/bcftools#2324 · 2 comments · 2 reactions · Opened Nov 26, 2024
Filter a gene list including intergenic regions Open

needs-feedback

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/bcftools#2319 · 3 comments · Opened Nov 12, 2024
Consensus of ALTs only without genotypes in file Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 40/100

samtools/bcftools#2315 · 2 comments · Opened Nov 9, 2024
seg fault for reheader -o Open

requires-test-case

Difficulty 3/5 1-2 days Newbie friendliness 64/100

samtools/bcftools#2311 · 4 comments · Opened Oct 30, 2024
Error "Failed to read from standard input: unknown file type" with Gzipped BAM Files Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/bcftools#2293 · 1 comment · Opened Sep 27, 2024

samtools/bcftools

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