samtools/bcftools

Issues

• The genotypes do not reflect the allele coverage frequency

  #2352 opened 8 days ago by pailloufat-stack
  0

• plot-vcfstats -s leads to IndexError: list index out of range

  #2353 opened 8 days ago by warthmann
  0

• bcftools stats does not return any information on the complements

  #2344 opened 8 days ago by laura-an
  2

• bcftools norm: Why did it "normalize" this deletion by shifting REF 5' by 29 bp?

  #2336 opened 9 days ago by toddajohnson
  2

• Feature request: norm --remove-duplicates report removed dupes in summary stats

  #2346 opened 9 days ago by davmlaw
  1

• Problems defining ploidy with bcftools call

  #2351 opened 9 days ago by amankowski
  0

• feature request: duplicate merging and selecting

  #2342 opened a month ago by davmlaw
  1

• consensus `--missing` not compatible with gvcf blocks

  #2350 opened 10 days ago by Fan-iX
  0

• mpileup's off-by-one bug: when cannot parse contig name with a comma, subsequent output is wrongly labeled

  #2345 opened a month ago by azaznaev
  2

• 1 bp insertion supported by deep sequencing missed by bcftools mpile/call

  #2343 opened a month ago by carolynzy
  1

• how to subset .vcf.gz file to include only variants whose genomic coordinates are given in a list

  #2332 opened a month ago by annilk
  5

• recovering multiallelics with bcftools norm is changing reference alleles to missing

  #2339 opened a month ago by bwspitzer
  2

• bcftools query: referencing ID column when there is a META field named ID?

  #2337 opened 14 days ago by bbimber
  2

• Problem with specifying filtering expression v1.21

  #2322 opened 14 days ago by reshu23
  6

• fill-tags VAF and VAF1 not working for multi-allelic sites

  #2338 opened 14 days ago by bartcharbon
  1

• Filter a gene list including intergenic regions

  #2319 opened 2 months ago by ccbruels
  3

• bcftools 1.20 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants

  #2333 opened 15 days ago by jcm6t
  3

• bcftools annotate labels transferred FILTER column as single value "Number=1" in header

  #2335 opened 15 days ago by toddajohnson
  1

• Bcftools query does not recognize arithmetic functions

  #2349 opened 17 days ago by smlchen
  0

• Error occurred while processing INFO tag "RPA" when use bcftools merge

  #2348 opened 18 days ago by TuBieJun
  0

• 2 lines of InDel in the same position ?

  #2347 opened 24 days ago by Jerry-Wang-Dog
  0

• Merge speed has not been increased by '--threads' option ?

  #2340 opened a month ago by Jerry-Wang-Dog
  2

• Empty filtering expression results in segfault

  #2341 opened a month ago by pd3
  0

• [E::hts_idx_push] Invalid record on sequence #2: end 1 < begin 2040518

  #2329 opened a month ago by ivan-adzhubey
  2

• Different parameters on different chromosomes

  #2327 opened 2 months ago by JJ0ONATHANESTAR
  1

• bcftools filter version 1.21 doesn't accept %QUAL

  #2334 opened a month ago by sinamajidian
  1

• bcftools csq Error: the fasta reference does not match the VCF REF allele at h2tg000007l:1000944

  #2323 opened a month ago by leon945945
  15

• bcftools merge remove the phase of half-missing genotypes

  #2331 opened a month ago by Han-Cao
  1

• strange handling of SVs by bcftools norm --fasta-ref

  #2330 opened a month ago by maggs-x
  3

• bcftools 1.21 merge segmentation fault

  #2328 opened a month ago by peterjuv
  2

• bcftools merge missing GT information

  #2326 opened a month ago by poddarharsh15
  5

• Majority of SNPs have allele frequency = 0.000000

  #2321 opened a month ago by ryanskiba
  4

• seg fault for reheader -o

  #2311 opened 3 months ago by Ahuiting
  3

• fail to find libgsl

  #2325 opened a month ago by caylamason
  3

• [Feature Request] Cannot sort using custom contig order

  #2324 opened 2 months ago by rickymagner
  2

• bcftools view -m 2 -M 2 referencePanel.vcf.gz（SV and SNP）

  #2320 opened a month ago by SunWinner01
  5

• bcftools: command does not work correctly. Can you help me?

  #2318 opened 2 months ago by jhownatan1
  4

• Bcftools view——locate problematic genotype in GT field

  #2309 opened a month ago by Lloyd-LiuSiyi
  7

• Error: bcftools csq --- splice_build_hap: Assertion `splice->tr->beg <= rbeg' failed.

  #2313 opened a month ago by sbgonenc
  1

• `bcftools norm` can not handle insertion-breakend entries with fasta reference (VCF4.3+)

  #2317 opened 2 months ago by Nicolai-vKuegelgen
  1

• Consensus of ALTs only without genotypes in file

  #2315 opened 2 months ago by schorlton-bugseq
  2

• cmp_vector_strings() in filter.c complains that nvalues!=str_value.l for VCF lines missing the GT format

  #2314 opened 2 months ago by freeseek
  1

• bcftools header check err

  #2312 opened 2 months ago by xiucz
  3

• Trying to understand mpileup output format

  #2308 opened 2 months ago by anderspitman
  4

• How to Generate Haplotype 1 and 2 FASTA Files Using Phased VCF from HiPhase

  #2310 opened 3 months ago by ClarenceHsiang
  1

• 'annotate' error message when trying to put a Float into an 'Number=A,type=Integer' INFO

  #2306 opened 3 months ago by Gullumluvl
  1

• Convert missing single dot to "./."?

  #2303 opened 3 months ago by bbimber
  2

• Heterozygocity missing

  #2304 opened 3 months ago by cottonrnr
  2

• bcftools annotate - tag ID not defined

  #2302 opened 3 months ago by ValentinaPeona
  3

• bcftools call empty output with -o

  #2301 opened 3 months ago by niederhuth
  3