How does bedtools operate VCF files

This article mainly explains "how to operate VCF files with bedtools". Interested friends may wish to have a look. The method introduced in this paper is simple, fast and practical. Let's let the editor take you to learn "how to operate VCF files by bedtools".

A mpileup function

Usage: bcftools mpileup [OPTIONS]-f ref.fa in.bam [in2.bam […]]

Example: bcftools mpileup-C 50-m 2-F 0.002-d 1000-Q 20-Q 20-a DP,DP4,ADR-f hg19.fa A.bam B.bam

Parameter description:

-f: specify the reference genome, followed by the bam file for mutation detection, which can be written directly when there is less bam.

Bcftools mpileup-f hg19.fa A.bam B.bam

-b: followed by a bamlist file

Bcftools mpileup-f hg19.fa-b bamList

-C-- the MQ value corrected by adjust-MQ INT is recommended to be 50

-Q,-min-MQ INT (MQ quality value) # filter MQ quality value

-Q,-- min-BQ INT (base quality value) # filter base quality value

-r,-- regions only call specific chromosomes, or dots, regions

The form is CHR | CHR:POS | CHR:FROM-TO | CHR:FROM- [, …]

Example: bcftools mpileup-r chr1-f hg19.fa A.bam | bcftools call-c-v > A.chr1.vcfbcftools mpileup-r chr1:111111-122222-f hg19.fa A.bam B.bam | bcftools call-c-v > A.chr1_111111-122222.vcf

-R,-- regions-file FILE when there is more than one region, save the region to the file, using the-R parameter. File format: three columns divided by tab, chr start end.

-a,-- annotate LIST adds some information such as DP,DP4,AD to the INFO/FORMAT column, and the group call may need

Comma-separated list of FORMAT and INFO tags to output.

Two bcftools call function

Usage: bcftools call [OPTIONS] FILE

Example: bcftools mpileup-f hg19.fa A.bam B.bam | bcftools call-c-v-r chr1:111111-122222-s A-V indels

The example shows:

Only A sample is detected, and only the SNP information of chr1:111111-122222 area is output, which is saved to test2.vcf file.

Parameter description:

-c-m is two ways of call. The old version uses-c, but now it uses-m by default, which can solve most tasks.

-V,-- skip-variants snps | indels skips SNP or INDEL sites

-v,-- variants-only outputs only the mutation site

-s,-- samples LIST only detects the sample ID given here (general parameter)

-S,-- samples-file FILE detects only the samples listed in this file (common parameters)

-r-R is a general parameter, which is consistent with the above usage

Triple bcftools filter function

Usage: bcftools filter [OPTIONS] FILE

Example: bcftools filter ALL.vcf TYPE= "snp"-e'DP < 20 | | MQ < 20 | |% QUAL