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
Hello, I have a very annoying problem and hope that you can help me. I have a vcf file containing appr 800 000 snps (with rs id) from 95 subjects....
Hello, thanks for maintaining bcftools! Would it be possible to allow the -i/-e flags to accept a text file containing the expression to perform inclusion/exclusion by? I'm aware that this...
I'm running bcftools 1.15.1 on Linux 4.18.0-372.16.1.el8_6.x86_64 on Red Hat 8.6 (Ootpa) with gcc version 8.5.0 I am running bcftools in a series of commands first I run `bcftools sort`...
Because the unseen star allele is not supported by `bcf_get_variant_types`, the command `bcftools view --types ref` is unable to distinguish between the star allele and other symbolic alleles, such as...
It would be great if bcftools stats could generate this output as well. I dont see it in the docs nor when I use bcftools stats. Tool works great though...
Hi, While using the +Mendellian plugin in bcftools v1.14 using the following command: `bcftools +mendelian -m + --trio Mother,Father,Proband input_GQ20_snpeff.vcf -O v -o output_GQ20_snpeff.vcf`, I am getting sites such as...
Dear developers, I am writing to you because it seems that bcftools stats does not take into account 2/2 type genotypes when calculating nNonRefHom in the counts per sample section....
Hi, I have genotyped a group of samples and then I used bcftools to exclude one which had a lot of missing data. I used the following code to do...
Hi, I am using bcftools consensus using v1.15 and got SNPs which were weirdly not called, so I went back to the vcf files. I have SNPs which I know...
Hi, I am using bcftools v1.14. I am working with trios and I was using bcftools +mendelian plugin in order to retain consistent records i.e. I wanted to retain sites...