This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Extract mutations for a specific gene from a vcf file

I downloaded more than 4000+ VCF files from TCGA but I am only interested in mutations of one gene, IDH1. I am wondering what is the best way to extract the mutations of this gene from these VCF files. Desired output would be a data matrix. Is there a vcf tools can realize this?

vcf
• 5,107 views • link
updated by Santosh Anand Santosh Anand • written by ddzhangzz ddzhangzz

I think you can use bedtools intersect here where the option -a would be a bed file for the coordinate of your interest gene and -b would be the vcf files

• 0 views • link
written by Medhat Medhat

If you're working with somatic mutations, you should download MAF file of each cohort rather than vcf for each patient/sample.

• 0 views • link
written by poisonAlien poisonAlien

2 answers

tabix is the best tool to extract regions of interest from vcf files

bgzip my.vcf # tabix works on block compressed data only (output my.vcf.gz)
tabix -p vcf my.vcf.gz # index vcf file 
tabix my.vcf.gz chr1:1-1000000

See other options of tabix http://www.htslib.org/doc/tabix.html

• 0 views • link
written by Santosh Anand Santosh Anand

If you know the coordinates of the gene, you could use awk or bedtools to get all mutations in a specific genomic interval.

• 0 views • link
written by swbarnes2 swbarnes2

Log in to answer this question.

More posts like this