retrieving from ExAC in VCF format

Question

[alessandrotestori7]

Hello! Is it possible to retrieve information about variants of a single gene from the ExAC Browser in VCF format? I can only see the option to "Export table to CSV".

[daniko07]

thank you for your advice!

Answer 1

[Vivek]

You can use tabix and query directly from the FTP:

tabix -h ftp://ftp.broadinstitute.org/pub/ExAC_release/current/ExAC.r0.3.1.sites.vep.vcf.gz 2:39967768-39967768 > exported.vcf

[alessandrotestori7]

Thanks a lot! It works perfectly

[daniko07]

Hello, is it possible to generate vcf files with tabix and exclude the 7601 samples deriving from the TCGA cohort in ExAC?

[Vivek]

There are tools like vcftools, GATK or bcftools that can achieve this:

This thread might be helpful: Extract subset of samples from multigenome vcf file

[daniko07]

I now have a VCF file and I would like to keep only the non-Finn European (NFE). I don't have a list of samples to keep, but I think this can be done by "INFO FIELD FILTERING" with VCFtools. In fact, I read lines like this: "##INFO=<id=an_nfe ..="" which="" are="" what="" i="" need.="" please="" let="" me="" know.="" thanks<="" p="">

[Vivek]

If its in the info fields, you can use GATK's SelectVariants utility. Here are some examples on using JEXL expressions to filter your VCF file: https://gatkforums.broadinstitute.org/gatk/discussion/1255/using-jexl-to-apply-hard-filters-or-select-variants-based-on-annotation-values

[daniko07]

Apologies, but maybe I have done some confusion above: I have looked at your link, but I'm afraid this is not very helpful for what I have to do. Basically I must keep only one subpopulation in my VCF file and in the info fields I have information about the populations. Now suppose I only want to keep one population in my vcf file (non Finn Europeans, NFE): is there an easy way to remove all the rest and keep only non finn europeans (maybe with vcftools)?

Answer 2

[daniko07]

I use the following command to annotate vcf files: table_annovar.pl example/ex2.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation g,r,f,f,f -nastring . -vcfinput

but unfortunately I see the COSMIC and CLINVAR annotations are missing. How can I include them? Please let me know. Thanks