bcftools
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samtools
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
This is a request for improved documentation. Doing a hunt through the documentation I find local alleles mentioned in one section only: ``` $ egrep -n -i "local.*allele" ../bcftools/doc/*.txt 2008:*-L,...
I could be very wrong. The syntax and threshold values in the example might be outdated in Filtering variants on https://samtools.github.io/bcftools/howtos/variant-calling.html: ``` bcftools filter -sLowQual -g3 -G10 \ -e'%QUAL
I'm not sure if I am misunderstanding how `bcftools +remove-overlaps` works, but I still have some overlapping variants in the output afterwards e.g., ``` chromosome 28728 62e866df T A ....
Dear developers, I am looking to generate a VCF file in which all positions of the reference are represented - so also those where my input bam has no read...
I am trying to run `bcftools sort` on a VCF for a species with long chromosomes (>2Gb), but have run into this error: ``` $ bcftools sort -o sample.vcf.gz -m...
Hi there, When using the merge command to combine VCFs from 60 individuals I am getting an output which includes non-identical variants being output to the same record without a...
Hi Peter, I wrote a simple parser for the consequences output by the `--local-csq` code. It turned out the haplotype-aware code outputs way different format. I am guessing there are...
Mention somewhere that multiallelic variants need to be expanded with e.g. `bcftools norm --multiallelics +both`, if you want to remove overlaps with `bcftools +remove-overlaps`. An entry that contain multiple mutations...
Hi Github community, I want to filter out homozygous, heterozygous and missing genotypes from **multi-sample single vcf file** and need to keep only polymorphic alleles. Kindly suggest which tool or...
Hello, I'm interesting in identify if my sample has a insertion, deletion or if it's heterozygote (in a specific region). To do this I ran the next code `bcftools mpileup...
