pulling snps from vcf file using ids
1
0
Entering edit mode
3.1 years ago
RNAseqer ▴ 200

Is there a command line in vcf tools to pull a subset of snps out of a vcf file based on their rs# ids?

vcf ids snps • 3.7k views
ADD COMMENT
7
Entering edit mode
3.1 years ago

Input list:

cat snps.list

rs575563330
rs572898889
rs141149254

Now filter with BCFtools:

bcftools-1.9/bcftools view --include ID==@snps.list 1000Genomes.Norm.bcf | cut -f 1-4

##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters="" passed"="">
##fileDate=20150218
##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
##source=1000GenomesPhase3Pipeline
##contig=<ID=1,assembly=b37,length=249250621>
##contig=<ID=2,assembly=b37,length=243199373>
##contig=<ID=3,assembly=b37,length=198022430>
##contig=<ID=4,assembly=b37,length=191154276>
... ...
##bcftools_viewVersion=1.9+htslib-1.9
##bcftools_viewCommand=view --include ID==@snps.list 1000Genomes.Norm.bcf; Date=Tue Apr  9 00:04:38 2019
#CHROM  POS ID  REF
1   54490   rs141149254 G
1   54531   rs572898889 C
1   54566   rs575563330 G

Kevin

ADD COMMENT
1
Entering edit mode

This worked beautifully, thanks!

ADD REPLY

Login before adding your answer.

Traffic: 1922 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6