To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Advanced Filtering of SNPS

yfarjounyfarjoun Broad InstituteDev


I'm looking for pairs of nearby SNPs with the following properties:

  1. of two given samples, one is HOM_REF at the locus while the other is HOM_VAR
  2. the locus is close to another with property 1. (say 50bp, but should be configuarable)

Any ideas how I could filter a VCF to obtain such a reduced subset? (I could write a walker, but was hoping to get some of the work done by an existing one)



Best Answers


  • yfarjounyfarjoun Broad InstituteDev

    ok. it would seem that two annotators could do this if run in series, one that finds the HOM_REF / HOM_VAR combination and the other that finds nearby SNPS....does either of these exist?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Not in the public toolbox, I think, but you're welcome to check the docs to make sure... And check private too just in case there's something experimental we haven't released yet.

  • yfarjounyfarjoun Broad InstituteDev

    Thanks for reminding me of JEXL expressions. I'll give it a try.

    I'm not sure I understand how your suggestions for step 2 would work. Assuming I have a .vcf with only 3 sites, two which are within 50bp and a third that is far, how does -L help me? after all, all three sites are already in the VCF!

  • The idea for -L is to only consider certain sites. So you'd only look at the Step 1 sites with -L, and then use -ip to expand it to nearby regions. It's the VCF equivalent of subsetting a BAM

Sign In or Register to comment.