vcf/bcfから必要なフィールドだけ問い合わせる bcftoolsのqueryコマンド

2020 10/14 タイトル変更

manual

http://samtools.github.io/bcftools/bcftools.html

BCFtools HowTo

bcftoolsのインストール

#bioconda (link)
conda install -c bioconda -y bcftools

> bcftools

# bcftools

Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)

Version: 1.8 (using htslib 1.8)

Usage: bcftools [--version|--version-only] [--help] <command> <argument>

Commands:

-- Indexing

index index VCF/BCF files

-- VCF/BCF manipulation

annotate annotate and edit VCF/BCF files

concat concatenate VCF/BCF files from the same set of samples

convert convert VCF/BCF files to different formats and back

isec intersections of VCF/BCF files

merge merge VCF/BCF files files from non-overlapping sample sets

norm left-align and normalize indels

plugin user-defined plugins

query transform VCF/BCF into user-defined formats

reheader modify VCF/BCF header, change sample names

sort sort VCF/BCF file

view VCF/BCF conversion, view, subset and filter VCF/BCF files

-- VCF/BCF analysis

call SNP/indel calling

consensus create consensus sequence by applying VCF variants

cnv HMM CNV calling

csq call variation consequences

filter filter VCF/BCF files using fixed thresholds

gtcheck check sample concordance, detect sample swaps and contamination

mpileup multi-way pileup producing genotype likelihoods

roh identify runs of autozygosity (HMM)

stats produce VCF/BCF stats

Most commands accept VCF, bgzipped VCF, and BCF with the file type detected

automatically even when streaming from a pipe. Indexed VCF and BCF will work

in all situations. Un-indexed VCF and BCF and streams will work in most but

not all situations.

> bcftools query

# bcftools query

About: Extracts fields from VCF/BCF file and prints them in user-defined format

Usage: bcftools query [options] <A.vcf.gz> [<B.vcf.gz> [...]]

Options:

-e, --exclude <expr> exclude sites for which the expression is true (see man page for details)

-f, --format <string> see man page for details

-H, --print-header print header

-i, --include <expr> select sites for which the expression is true (see man page for details)

-l, --list-samples print the list of samples and exit

-o, --output-file <file> output file name [stdout]

-r, --regions <region> restrict to comma-separated list of regions

-R, --regions-file <file> restrict to regions listed in a file

-s, --samples <list> list of samples to include

-S, --samples-file <file> file of samples to include

-t, --targets <region> similar to -r but streams rather than index-jumps

-T, --targets-file <file> similar to -R but streams rather than index-jumps

-u, --allow-undef-tags print "." for undefined tags

-v, --vcf-list <file> process multiple VCFs listed in the file

Examples:

bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz

> bcftools view

# bcftools view

About: VCF/BCF conversion, view, subset and filter VCF/BCF files.

Usage: bcftools view [options] <in.vcf.gz> [region1 [...]]

Output options:

-G, --drop-genotypes drop individual genotype information (after subsetting if -s option set)

-h/H, --header-only/--no-header print the header only/suppress the header in VCF output

-l, --compression-level [0-9] compression level: 0 uncompressed, 1 best speed, 9 best compression [-1]

--no-version do not append version and command line to the header

-o, --output-file <file> output file name [stdout]

-O, --output-type <b|u|z|v> b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]

-r, --regions <region> restrict to comma-separated list of regions

-R, --regions-file <file> restrict to regions listed in a file

-t, --targets [^]<region> similar to -r but streams rather than index-jumps. Exclude regions with "^" prefix

-T, --targets-file [^]<file> similar to -R but streams rather than index-jumps. Exclude regions with "^" prefix

--threads <int> number of extra (de)compression threads [0]

Subset options:

-a, --trim-alt-alleles trim alternate alleles not seen in the subset

-I, --no-update do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)

-s, --samples [^]<list> comma separated list of samples to include (or exclude with "^" prefix)

-S, --samples-file [^]<file> file of samples to include (or exclude with "^" prefix)

--force-samples only warn about unknown subset samples

Filter options:

-c/C, --min-ac/--max-ac <int>[:<type>] minimum/maximum count for non-reference (nref), 1st alternate (alt1), least frequent

(minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]

-f, --apply-filters <list> require at least one of the listed FILTER strings (e.g. "PASS,.")

-g, --genotype [^]<hom|het|miss> require one or more hom/het/missing genotype or, if prefixed with "^", exclude sites with hom/het/missing genotypes

-i/e, --include/--exclude <expr> select/exclude sites for which the expression is true (see man page for details)

-k/n, --known/--novel select known/novel sites only (ID is not/is '.')

-m/M, --min-alleles/--max-alleles <int> minimum/maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)

-p/P, --phased/--exclude-phased select/exclude sites where all samples are phased

-q/Q, --min-af/--max-af <float>[:<type>] minimum/maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent

(minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]

-u/U, --uncalled/--exclude-uncalled select/exclude sites without a called genotype

-v/V, --types/--exclude-types <list> select/exclude comma-separated list of variant types: snps,indels,mnps,ref,bnd,other [null]

-x/X, --private/--exclude-private select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples

実行方法

テストデータ

#test data
git clone https://github.com/samtools/bcftools.git
cd bcftools/test/

bcftools view

先にvcf <=> bcf変換などができるbcftools viewをまとめておく（他にも機能あり）。

#vcf => bcf
bcftools view -Ou input.vcf -o output.bcf 

#bcf => vcf
bcftools view -Ov input.bcf -o output.vcf

#vcf => vcf.gz
bcftools view -Oz input.vcf -o output.vcf.gz

#bcf => vcf.gz
bcftools view -Oz input.bcf -o output.vcf.gz

#vcf => compressed bcf
bcftools view -Ob input.vcf -o output.bcf.gz

#bcf => compressed bcf
bcftools view -Ob input.bcf -o output.bcf.gz

#indexing（tabix）installするにはhtslibをビルドするかcondaを使う（*1）
tabix -p vcf output.vcf.gz
=> output.vcf.gz.tbiができる

#BGZF compressin and create index (bgzip)installするにはhtslibをビルドするかcondaを使う（*2）
bgzip -i output.bcf
=> output.bcf.gz.gbiができる(-@ 4だと４スレッド使用)

-O <b|u|z|v> b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]

bcftools query

vcf/bcfに含まれるサンプルのリスト

#-lをつけて実行
bcftools query -l mpileup.vcf

-l print the list of samples and exit

# bcftools query -l mpileup.vcf

HG00100

HG00101

HG00102

VCFの必要なフィールドだけ取り出す。シンプルなタブ区切りリストに変換されるので、全てのフィールドを指定することでVCF/BCF => タブ区切り変換コマンドとしても機能する。

#bcf/vcfからPOSフィールドだけ取り出す
bcftools query -f '%POS\n' file.bcf

#chr、positon、 ref, alt（allele）だけ取り出す。
bcftools query -f '%CHROM %POS %REF %ALT\n' file.vcf

#FORMATタグの一部を取り出す場合は[]で囲んで指定
bcftools query -f '%CHROM %POS[\t%AF\t%DP]\n' file.bcf

#手動で全てのフィールドを指定（異なるフィールドがあれば修正してください）
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t[\t%AC\t%AF\t%AN\t%BaseQRankSum\t%DP\t%ExcessHet\t%FS\t%MLEAF\t%MQ\t%MQRankSum\t%QD\t%ReadPosRankSum\t%SOR\t%ANN]\n' inpuy.bcf.gz