extract vcf subinfo

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8.8 years ago

jan.breitling ▴ 10

Hi

The vcf file I am using is here: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/vcf_with_sample_level_annotation/

It is a annotated vcf fort the 1000G. I am looking to extract the following information

-Position of LOF mutations -Position of Coding mutations -Position of functional noncoding -Position of unannotated vars

I really don't know how to do that - is there any simple way to to do that? I would be really grateful! Like in awk, python, R or so?

R SNP • 2.0k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 8.8 years ago by jan.breitling ▴ 10

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Try Annovar or KGGSeq

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 8.8 years ago by Sam ★ 4.8k

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well - sorry but how does that help?

ADD REPLY • link 8.8 years ago by jan.breitling ▴ 10

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Those two programme can annotate all the SNPs within the VCF. Based on the annotation, you can then filtered out all the LOF mutations, Coding mutations etc.

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 8.8 years ago by Sam ★ 4.8k

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