Filtering multi-sample VCFs for low DP

DavyK1984

Hi Team,

I have a multi-sample VCF file produced by UnifiedGenotyper. I now want to filter this file marking those variants with a low depth. However the DP entry in the info field is across all samples, and even if it were possible to assess the individual's DPs, I would then have to resolve the issue of a variant having low depth in one sample, and high in another. Any suggestions are appreciated.

Thanks for your time

Geraldine_VdAuwera

I'm guessing you used the --filterExpression argument; that only looks at INFO field annotations. I think what you want is --genotypeFilterExpression, which looks at FORMAT field annotations.

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_filters_VariantFiltration.html

ebanks

Try using the DP from the sample fields.

DavyK1984

That is what I was looking to do, but when I used DP in a JEXL expression it seems to only look at the aggregate depth. I have been looking through the documentation for VariantFiltration and VariantAnnotator, but can't find how to do this.

DavyK1984

Excellent! Thanks a million.

ami

Just in case you still need help with that issue, I just wrote a walker that allow you to print out the sites (as intervals) that more than X% of them have at list Y coverage (based on their DP as Eric suggested). This walker will be part of the next release.

ecuenca

Hi Ami, I'm very interested in to apply that filter (to print out the sites from which 90% of samples have more than x DP). Do you now when the next release is going to be available? Thanks a lot.

Geraldine_VdAuwera

The new version will come out very soon -- today if things go to plan.

ecuenca

Great! Thanks a lot, Ester

ecuenca

Hi, I have already downloaded the new version. Could you please tell me which is the walker that allows you to print out the sites with more than x DP in x% of samples? Thanks a lot!

ami

Hi,

The new walker is called CoveredByNSamplesSites and I hope it will help you in your tasks. As far as I know, I'm the only one that used it so far and it was before most of the changes in the last GATK version were done, so please try it and let me know if you find any problems with it. http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_diagnostics_CoveredByNSamplesSites.html

ecuenca

Hi Ami, sorry I didn't realized that you had answered me (I usually receive an e-mail). The job is now running, I let you know at the end of the day. There is typo in the GATK documentation: --precentageOfSamples Thanks a lot, Best,

ecuenca

Hi Ami, no problems using this walker with the new version of GATK. It works perfectly! Thank you very much! Best,

ami

Thanks for letting us know (both that it works fine and about the typo).

evakoe

As stated in the documentation of VariantFiltration for the --genotypeFilterExpression tag, "VariantFiltration will add the sample-level FT tag to the FORMAT field of filtered samples (this does not affect the record's FILTER tag). "

My question is: How can I select variants from my VariantFiltration output vcf file using the information that was written in the FORMAT FT tag by Variant Filtration? I did not see an option for this in SelectVariant with which I can only select variants which have FILTER == PASS

Is there a GATK option / tool for that? Thank you. Eva

Geraldine_VdAuwera

Hi Eva,

There is no built-in tool to do this. You'll need to use a JEXL expression using Variant Context methods. I think it's something like vc.isFiltered(). Let me know if that doesn't work, I'll help you find the right one.

evakoe

Thanks for the info Geraldine, I think I'll manage.