samtools / bcftools

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

http://samtools.github.io/bcftools/

samtools/bcftools Issues

Change GVCFBlocks (+gvcfz) and header
Updated 15 days ago1
bcftools concat issues...
Closed 15 days ago4
Bcftools mpileup
Updated 15 days ago1
How does bcftools merge determine whether the genotype is 0/0 or ./. ?
Updated 15 days ago1
[mpileup2] How does mpileup choose the reads for later calling, and is the -d flag behaving strangely?
Updated 15 days ago1
bcftools call -A => segmentation fault
Updated 15 days ago3
norm remove dupes doesn't handle symbolic and non-symbolic duplicates
Updated 15 days ago4
Plugin +mendelian2 reports missing samples incorrectly
Updated 17 days ago
setGT plugin bug when filtering with FMT/DHFFC or FMT/DHBFC
Updated 18 days ago
The INDEL/TR variant rs746071566 was not called by Bcftools v1.20 with --indels-cns in mpileup
Updated 18 days ago
Multi-allelic and complex variants lose zygosity info when atomized
Updated 20 days ago
Add --verbosity flag like samtools
Updated 20 days ago1
How does mpileup adjust-MQ actually work?
Updated 22 days ago6
Manual typo in bcftools call -g
Closed a month ago2
bcftools call only sometimes outputs the `INFO/HWE` and `INFO/G3` fields
Closed a month ago2
Merge adjacent sites into a complex
Updated a month ago1
bcftools 1.20 merge (--merge both) gvcfs results in more than one variant at the same location for very complex polyallelic MNP variants
Closed a month ago1
norm --remove-duplicates should keep the --old-rec-tag INFO field
Closed a month ago1
how to use plot-roh.py to draw the plot by using the "bcftools roh" output
Closed a month ago1
bcftools sort (and maybe bcftools merge as well) "Too many open files" error
Updated a month ago
bcftools convert --tag bug
Closed a month ago1
snp number issue
Closed a month ago1
bcf can't parse vcf files: bcf_hdr_parse_sample_line error
Closed a month ago1
How does bcftools isec identify the same sites
Updated a month ago1
Find unique SNP in a sample from a multisample VCF file
Closed a month ago1
bcftools norm shifts symbolic <DEL> to position 1 without warning if the END tag is missing from VCF
Updated a month ago1
There could be a mistake in bcftools/mpileup_bench/get_data.sh
Updated a month ago
Is there a way to filter on fraction of reads supporting an allele?
Closed a month ago2
CSQ annotation - should be frameshift
Closed 2 months ago4
Bcftools view -i sMIN(FORMAT/DP)>=3 error
Closed 2 months ago2
Possible isec memory leak
Closed 2 months ago1
[Solved] bcftools merge Failed to open *vcf.gz: could not load index
Closed 2 months ago1
Genotype Hard Calling- keeping GQ>=20, DP >=10 and 0.2<AB<0.8
Closed 2 months ago5
Merge error - duplicate sample names
Closed 2 months ago1
GTcheck discrepancy between discordance score and the number of matching genotypes
Closed 2 months ago1
BCFtools not calling variant, despite adequate coverage
Closed 2 months ago3
Problem with plugin tests
Updated 2 months ago
Speeding up bcftools merge for large number of vcf files with identical variant records containing sample genotypes.
Closed 2 months ago1
Clarification on -e 0 flag and interpretation of discordance with PL-vs-PL and GT-vs-GT
Closed 3 months ago3
Ability to skip nonvariant records within a trio for mendelian2 plugin
Closed 2 months ago1
bcftools concat --allow-overlaps produces output VCF with contigs out of order
Closed 3 months ago5
How to count number of haplotypes and haplotype frequency from phased vcf files?
Closed 3 months ago1
bcftools annotate can output an INFO field with unquoted semicolons
Closed 3 months ago1
Apart from the header, bcftools mpileup did not output any other content
Closed 3 months ago5
[merge] [view] Feature request: Ability to delete an unseen allele line if it duplicates an ALT-containing line
Closed 3 months ago4
How to compare several vcf files using bcftools
Closed 3 months ago2
Undefined header [W::vcf_parse] INFO 'PR' is not defined in the header, assuming Type=String
Closed 3 months ago1
Renaming .vcf.gz file using mv command and now bcftools won't recognise
Closed 3 months ago1
consensus `>chr1:1-1` leads to error `FIXME: <chr>:<pos> .. idx=-<int>, ori_pos=<pos>`
Closed 3 months ago1
Substring matching for variant IDs to aid in filtering records with multiple IDs?
Closed 3 months ago1