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
Hi All, Second time lucky (first pull request was polluted with stuff). It appears to me there's a pretty serious flaw with GT flag splitting in the normalisation. This is...
Dear Samtools team, do you support VCFs exported from QIAGEN CLC genomics workbench? QIAGEN CLC genomics workbench is able to represent complex overlapping variants in recommended `reference overlap` format ([https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/1203/index.php?manual=Complex_variant_representations_VCF_reference_overlap.html#fig:vcfoption](https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/1203/index.php?manual=Complex_variant_representations_VCF_reference_overlap.html#fig:vcfoption))...
I am trying to run PSMC to obtain demographic history, and am looking to call consensus sequences from my study samples. PSMC requires a ".fq.gz" input which is typically the...
I ran similar commands with the same data, only changing the -H setting. `bcf consensus -H 1 -f reference.fa subject.vcf.gz > consensus_H1.fasta` `bcf consensus -H 2 -f reference.fa subject.vcf.gz >...
Hiya - I've been trying to use mpileup and call with a file of regions to exclude from the call command, like so: `bcftools mpileup -Ou -f reference.fa input.bam |...
when I use `bcftools merge -l vcf.txt ">" merge.vcf` which vcf.txt contain /path/to/vcf what I want to merge . I found a BUG for example: > chr1 2595306 . C...
Many tools in bioinformatics provide a multilinux binary, which is a very convenient solution: very simple and reproducible installation, binaries are quite small anyway (and if they were big -...
Hi, I have two VCF files and want to calculate genotype concordance on a per samples basis. The two VCF files contain only the genotype values that were imputed based...
Hi, I'm wondering if there is a best practice for converting a multi-sample VCF file to a multi-sample FASTA using bcftools. I'm interested in generating a FASTA of variant sites...
hi I want to use bcftools to call dbsnp variants, here is my command # creage targets, dbsnp chrom is GRCh37-like ```bash bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' dbsnp138.vcf.gz \ | bgzip -c...
