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303 Open 1,652 Closed
303 Open 1,652 Closed
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Issues list

Warning: fewer CSQ fields than expected
#2295 opened Sep 28, 2024 by kuaileshizuihao
bcftools csq: Change chromosome name requirement.
#2294 opened Sep 28, 2024 by niederhuth
Error "Failed to read from standard input: unknown file type" with Gzipped BAM Files
#2293 opened Sep 27, 2024 by Silvia-lme
Sampling frequency field not found in the header. Please check the header fields.
#2292 opened Sep 27, 2024 by wahibalkamat2
BCFtools norm dropping duplicates options: is -d none equivalent to -d exact and -D ?
#2291 opened Sep 26, 2024 by davidjakubosky
Is BCFtools norm guaranteed to maintain sort order?
#2290 opened Sep 26, 2024 by davidjakubosky
How to populate Fisher test annotation
#2287 opened Sep 26, 2024 by pd3
1
bcftools concat segfault if VCF files contain only headers htslib-dependent Cannot be fixed until htslib is fixed
#2286 opened Sep 26, 2024 by dpryan79
2
Document / Improve / Polish / Fix --indels-2.0 bug D1: Difficult enhancement P2: Desirable
#2280 opened Sep 17, 2024 by jkbonfield
2
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
Extract a list of mean values from format tags (e.g., DP, GC, IGC, etc.) per position enhancement
#2271 opened Aug 30, 2024 by andreasgoteson
3
annotate ID for multi-allelic sites
#2264 opened Aug 20, 2024 by ikarus97
1
Remove the * ALT Allele Reporting From a g.vcf Before (or After) Genotyping
#2258 opened Aug 14, 2024 by jon4thin
1
bcftools mpileup resulting in downstream unparsable vcf record with allele M needs-feedback
#2256 opened Aug 13, 2024 by anscholes
1
bcftools norm -m +any replaces reference allele GTs with missing for repeated sites
#2247 opened Aug 7, 2024 by rickymagner
write-index does not appear to work from concat command
#2246 opened Aug 7, 2024 by ASLeonard
2
@whitwham
1
bcftools concat retry mechanisms? htslib-dependent Cannot be fixed until htslib is fixed
#2245 opened Aug 6, 2024 by graphenn
2
Bcftools mpileup needs-feedback
#2237 opened Jul 26, 2024 by Mashindersingh
1
Add --verbosity flag like samtools
#2235 opened Jul 25, 2024 by pettyalex
1
[mpileup2] How does mpileup choose the reads for later calling, and is the -d flag behaving strangely? D1: Difficult enhancement htslib-dependent Cannot be fixed until htslib is fixed
#2234 opened Jul 25, 2024 by goeckeritz
1
There could be a mistake in bcftools/mpileup_bench/get_data.sh
#2232 opened Jul 24, 2024 by zengxiaofei
1
4
How does bcftools isec identify the same sites
#2230 opened Jul 23, 2024 by ym-chen
1
Merge adjacent sites into a complex D1: Difficult P2: Desirable
#2229 opened Jul 19, 2024 by xfk274280
1
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