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310 Open 1,682 Closed
310 Open 1,682 Closed
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Issues list

bcftools query: referencing ID column when there is a META field named ID?
#2337 opened Dec 13, 2024 by bbimber
bcftools norm: Why did it "normalize" this deletion by shifting REF 5' by 29 bp?
#2336 opened Dec 13, 2024 by toddajohnson
bcftools annotate labels transferred FILTER column as single value "Number=1" in header
#2335 opened Dec 13, 2024 by toddajohnson
bcftools filter version 1.21 doesn't accept %QUAL
#2334 opened Dec 11, 2024 by sinamajidian
bcftools 1.20 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants
#2333 opened Dec 9, 2024 by jcm6t
how to subset .vcf.gz file to include only variants whose genomic coordinates are given in a list
#2332 opened Dec 9, 2024 by annilk
2
strange handling of SVs by bcftools norm --fasta-ref requires-test-case
#2330 opened Dec 6, 2024 by maggs-x
3
[E::hts_idx_push] Invalid record on sequence #2: end 1 < begin 2040518
#2329 opened Dec 4, 2024 by ivan-adzhubey
Different parameters on different chromosomes
#2327 opened Dec 1, 2024 by JJ0ONATHANESTAR
1
[Feature Request] Cannot sort using custom contig order enhancement
#2324 opened Nov 26, 2024 by rickymagner
2
Problem with specifying filtering expression v1.21
#2322 opened Nov 20, 2024 by reshu23
4
Filter a gene list including intergenic regions
#2319 opened Nov 12, 2024 by ccbruels
3
Consensus of ALTs only without genotypes in file enhancement
#2315 opened Nov 9, 2024 by schorlton-bugseq
2
seg fault for reheader -o requires-test-case
#2311 opened Oct 30, 2024 by Ahuiting
3
How to Generate Haplotype 1 and 2 FASTA Files Using Phased VCF from HiPhase
#2310 opened Oct 24, 2024 by ClarenceHsiang
1
bcftools annotate - tag ID not defined
#2302 opened Oct 15, 2024 by ValentinaPeona
3
Issue with bcftools annotate
#2297 opened Sep 30, 2024 by HVHunt
1
bcftools csq: Change chromosome name requirement.
#2294 opened Sep 28, 2024 by niederhuth
1
Error "Failed to read from standard input: unknown file type" with Gzipped BAM Files
#2293 opened Sep 27, 2024 by Silvia-lme
1
How to populate Fisher test annotation
#2287 opened Sep 26, 2024 by pd3
1
Document / Improve / Polish / Fix --indels-2.0 bug D1: Difficult enhancement P2: Desirable
#2280 opened Sep 17, 2024 by jkbonfield
3
Significant difference between IDV and AD when calling certain RNA-seq indels with mpileup
#2277 opened Sep 12, 2024 by luyh-xp
2
8
Variable expansion issue with +setGT? [$VARIABLE-] isn't working...
#2276 opened Sep 9, 2024 by goeckeritz
1
annotate add INFO/tag form CHROM-POS-REF-ALT
#2273 opened Sep 6, 2024 by user-tq
annotate ID for multi-allelic sites
#2264 opened Aug 20, 2024 by ikarus97
1
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