bedtoolsを使う。
Document
bedtoolsのインストール
本体 Github
#bioconda(link)
condaw install -c bioconda -y bedtools
> bedtools maskfasta
$ bedtools maskfasta
Tool: bedtools maskfasta (aka maskFastaFromBed)
Version: v2.29.0
Summary: Mask a fasta file based on feature coordinates.
Usage: bedtools maskfasta [OPTIONS] -fi <fasta> -fo <fasta> -bed <bed/gff/vcf>
Options:
-fi Input FASTA file
-bed BED/GFF/VCF file of ranges to mask in -fi
-fo Output FASTA file
-soft Enforce "soft" masking.
Mask with lower-case bases, instead of masking with Ns.
-mc Replace masking character.
Use another character, instead of masking with Ns.
-fullHeader Use full fasta header.
By default, only the word before the first space or tab
is used.
実行方法
入力の FASTAとマスクしたい領域のBED/GFF/VCFを指定して実行する。
bedtools maskfasta -fi input.fa -fo mask.fa -bed regions.bed
出力
ソフトマスク
bedtools maskfasta -fi input.fa -fo mask.fa -bed regions.bed -soft
出力
引用
BEDTools: a flexible suite of utilities for comparing genomic features.
Quinlan AR1, Hall IM.
Bioinformatics. 2010 Mar 15;26(6):841-2.
https://www.ncbi.nlm.nih.gov/pubmed/20110278
関連
