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Issues list

last version in apt
#2358 by BenjaminDEMAILLE was closed Jan 22, 2025
1
consensus --missing not compatible with gvcf blocks
#2350 by Fan-iX was closed Jan 25, 2025
1
Bcftools query does not recognize arithmetic functions
#2349 by smlchen was closed Jan 22, 2025
1
Error occurred while processing INFO tag "RPA" when use bcftools merge
#2348 by TuBieJun was closed Jan 22, 2025
1
Feature request: norm --remove-duplicates report removed dupes in summary stats
#2346 by davmlaw was closed Jan 8, 2025
1
bcftools stats does not return any information on the complements
#2344 by laura-an was closed Jan 9, 2025
2
1 bp insertion supported by deep sequencing missed by bcftools mpile/call
#2343 by carolynzy was closed Jan 10, 2025
2
Empty filtering expression results in segfault
#2341 by pd3 was closed Dec 17, 2024
fill-tags VAF and VAF1 not working for multi-allelic sites
#2338 by bartcharbon was closed Jan 2, 2025
1
bcftools query: referencing ID column when there is a META field named ID?
#2337 by bbimber was closed Jan 2, 2025
2
bcftools norm: Why did it "normalize" this deletion by shifting REF 5' by 29 bp?
#2336 by toddajohnson was closed Jan 8, 2025
2
bcftools annotate labels transferred FILTER column as single value "Number=1" in header
#2335 by toddajohnson was closed Jan 1, 2025
1
bcftools filter version 1.21 doesn't accept %QUAL
#2334 by sinamajidian was closed Dec 16, 2024
1
bcftools 1.20 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants requires-test-case
#2333 by jcm6t was closed Jan 2, 2025
3
bcftools merge remove the phase of half-missing genotypes
#2331 by Han-Cao was closed Dec 11, 2024
1
[E::hts_idx_push] Invalid record on sequence #2: end 1 < begin 2040518
#2329 by ivan-adzhubey was closed Dec 16, 2024
2
bcftools 1.21 merge segmentation fault
#2328 by peterjuv was closed Dec 11, 2024
2
bcftools merge missing GT information
#2326 by poddarharsh15 was closed Dec 3, 2024
5
fail to find libgsl
#2325 by caylamason was closed Dec 4, 2024
3
bcftools csq Error: the fasta reference does not match the VCF REF allele at h2tg000007l:1000944 requires-test-case
#2323 by leon945945 was closed Dec 11, 2024
15
Problem with specifying filtering expression v1.21
#2322 by reshu23 was closed Jan 2, 2025
6
Majority of SNPs have allele frequency = 0.000000 requires-test-case
#2321 by ryanskiba was closed Dec 4, 2024
4
bcftools view -m 2 -M 2 referencePanel.vcf.gz（SV and SNP）
#2320 by SunWinner01 was closed Dec 3, 2024
5
bcftools: command does not work correctly. Can you help me?
#2318 by jhownatan1 was closed Nov 18, 2024
4
bcftools norm can not handle insertion-breakend entries with fasta reference (VCF4.3+) htslib-dependent Cannot be fixed until htslib is fixed
#2317 by Nicolai-vKuegelgen was closed Nov 19, 2024
1
1
ProTip! Exclude everything labeled bug with -label:bug.