Linux command
bcftools 命令
文件
复制后可按需替换文件名、目录或参数。
常用示例
View a VCF/BCF file
bcftools view [input.vcf.gz]
Filter variants
bcftools view -r [chr1:1000000-2000000] [input.vcf.gz]
Convert VCF to BCF
bcftools view -Ob -o [output.bcf] [input.vcf.gz]
Call variants
bcftools mpileup -f [reference.fa] [aligned.bam] | bcftools call -mv -Oz -o [calls.vcf.gz]
Merge multiple VCF files
bcftools merge [file1.vcf.gz] [file2.vcf.gz] -Oz -o [merged.vcf.gz]
Filter variants
bcftools filter -i 'QUAL>30 && DP>10' [input.vcf.gz] -Oz -o [filtered.vcf.gz]
Extract sample genotypes
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT]\n' [input.vcf.gz]
Index a VCF/BCF file
bcftools index [input.vcf.gz]
说明
bcftools is a suite of utilities for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. It is part of the SAMtools/HTSlib project and is widely used in bioinformatics for genomic variant analysis. All commands work transparently with both VCF and BCF files, compressed or uncompressed. The tools are designed to work in pipelines, reading from stdin and writing to stdout.
参数
- -Ob
- Output compressed BCF
- -Oz
- Output compressed VCF (bgzipped)
- -Ov
- Output uncompressed VCF
- -Ou
- Output uncompressed BCF (fastest for piping)
- -r _region_
- Restrict to regions (chr:from-to format)
- -s _samples_
- Comma-separated list of samples to include
- -i _expression_
- Include sites matching filter expression
- -e _expression_
- Exclude sites matching filter expression
- -o _file_
- Output file name
FAQ
What is the bcftools command used for?
bcftools is a suite of utilities for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. It is part of the SAMtools/HTSlib project and is widely used in bioinformatics for genomic variant analysis. All commands work transparently with both VCF and BCF files, compressed or uncompressed. The tools are designed to work in pipelines, reading from stdin and writing to stdout.
How do I run a basic bcftools example?
Run `bcftools view [input.vcf.gz]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -Ob do in bcftools?
Output compressed BCF