BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe.

New bcftools head subcommand for conveniently displaying the headers of a VCF or BCF file. Without any options, this is equivalent to bcftools view --header-only --no-version but more succinct and memorable.

2021年3月12日 · BCFtools 是一款多种实用工具的集合，它可以用于处理VCF文件和二进制的BCF文件。 它可以接受VCF格式、压缩的VCF格式以及BCF格式，并能自动检测输入的格式类型。 在有索引文件存在的条件下，BCFtools 可以应用于所有场景，在没有索引文件存在时，BCFtools只能应用于部分场景。 通常，在同时读取多个VCFs时，必须对它们建立索引和压 …

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

This is the official development repository for BCFtools. It contains all the vcf* commands which previously lived in the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of samtools. For a full documentation, see bcftools GitHub page.

This is the official development repository for BCFtools. The latest versioned release can be downloaded from www.htslib.org. The most up to date (development) version of BCFtools can be obtained from github as described here.

BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

2025年3月19日 · bcftools norm --check-ref ws -f ref.fa in.vcf.gz -o out.vcf.gz -Oz // #changing the sample names in a VCF: #the samplenames.txt file has the following format: #oldsamplename newsamplename: bcftools reheader -s samplenames.txt NA12878.giab.SNP.chr20.non_valid.vcf.gz -o …

BCFtools is a very popular programme to call SNPs and genotypes (and also to manipulate and filter vcf/bcf files as we will see afterwards). SNP calling is a relatively intensive process, to speed things up we will be restricting variant calling to 3 scaffolds.

2025年3月12日 · Bcftools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. Adjust slurm options based on job requirements (slurm cheat sheet):