Using ExAC data with hg19

[alexholman]

I'm working on a project in which I'd like to annotate a VCF with features from the ExAC database. The VCF was generated with GATK against the hg19 reference, with naming conventions chr1 chr2 ... etc. The ExAC database uses GRCh37/hg19 (http://exac.broadinstitute.org/faq), however, it follows the naming convention 1, 2 ... etc which suggests b37. But the link off the ExAC site goes to a broad address with the file Homo_sapiens_assembly19.fasta.

When I try to do a liftover with the GATK LiftoverVariants tool with b37tohg19.chain I get the error
"Bad input: the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference"

The ExAC data only contains variants for 1-22, X and Y. Can I simply rename the chromosomes to chr1 etc and count on hg19 == hg19? Any suggestions on how to verify that the ExAC reference genome == the Broad GATK resource pack hg19 genome?

Thanks
Alex

[amruta.bn]

Hi ,

I am Bioinformatics enthusiast from India.It will be really helpful if you can answer below questions.


1. I have downloaded the vcf files from following link. ftp://ftp.broadinstitute.org/pub/ExA...se/release0.3/. I would like to know whether its the latest version?
I can see a version named current (ftp://ftp.broadinstitute.org/pub/ExAC_release/current ). Is current is the latest one ?


2. There are many different types of vcf files mainly :


ExAC.r0.3.nonTCGA.sites.vep.vcf.gz , ExAC.r0.3.nonpsych.sites.vcf.gz, ExAC.r0.3.sites.vep.vcf.gz and Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.

What is the difference between all these files.?
Can I say that nonTCGA.sites.vep.vcf.gz contain healthy individuals?
Is ExAC.r0.3.sites.vep.vcf.gz file a consolidated file?
What type of data the other two files contain?
Do you have a variant count for all these files?


3. Can you please give me a insight about functional gene constraint ?