Find common entries between VCF and ClinVar VCF

Question

[win]

hi all, i annotated a VCF file with ClinVar annotations and that worked fine. What I am interested to know is which entries in my VCF files were annotated with entries from ClinVar. In other words I am interested in know which of variants have any clinical significance.

Would VCF compare be the right approach? Any help will be highly appreciated.

Thanks in advance.

Answer 1

[Sean Davis]

If you added clinvar annotations to your VCF file, then using something like snpSift, GATK selectvariants, or VariantAnnotation package in Bioconductor to filter out variants with the CLINSIG you want.

Answer 2

[Damianos P. Melidis]

Hey, you can also do this intersection using Python. To do that I have followed the following steps:

1) Download clinvar.vcf.gz and clinvar.vcf.gz.tbi from ncbi

2) Install and import pyvcf from pyvcf

3) Load clinvar vcf into a new pvcf Reader object

4) Then reading your sample vcf file through an iterator giving you an tuple (chr, start, end) do a reader.fetch().

Please see more usages of pyvcf from its readthedocs

Hope it helps!