SnpSift: Annotate vcf file using GNOMAD
0
0
Entering edit mode
7 weeks ago
bsmith030465 ▴ 190

Hi,

I am trying to annotate my vcf file (my.vcf.gz) with gnomad using SnpEff/SnpSift. I downloaded gnomad (3.1.1) as given in the instructions GNOMAD download

I now want to annotate my vcf.gz file, containing variants from all chromosomes, with this data. The SnpSift example page SnpSift gives the example:

java -jar SnpSift.jar annotate dbSnp132.vcf variants.vcf > variants_annotated.vcf

However, the vcf file downloaded from gnomad is not a single file, but one file for each chromosome. For example:

gnomad.genomes.v3.1.1.sites.chr10.vcf.bgz.tbi gnomad.genomes.v3.1.1.sites.chr19.vcf.bgz.tbi gnomad.genomes.v3.1.1.sites.chr5.vcf.bgz.tbi

What command do I need so that it uses all the vcfs in the downloaded gnomad directory?

Thanks for your help!

GNOMAD SnpEff SnpSift • 180 views
ADD COMMENT
0
Entering edit mode

What command do I need so that it uses all the vcfs in the downloaded gnomad directory?

run a loop perv chromosome in your vcf and then concatenate each resulting vcf/chromosome

ADD REPLY

Login before adding your answer.

Traffic: 1007 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