Lower GATK's HaplotypeCaller threshold for allele frequency as part of variant calling pipeline

Question

[alons]

Hi all!

As part of a variant calling pipeline for cancer I'm interested in lowering the threshold for allele frequency tolerance in GATK's HaplotypeCaller variant caller to 0.01 (1%).

Background: I know for a fact that there's at least one variant in my sample that doesn't appear in my VCF files if allele frequencies below 0.1 (10%) are filtered out during the variant calling as it's the default in some of the programs. I can see the variant when I inspect the corresponding bam file with samtools tview and Agilent's SureCall program called it itself.

Now, I've managed to get that variant using freebayes by executing the following, essentially lowering the allele frequency threshold to 0.01:

freebayes -f ref.fa -F 0.01 -C 1 --pooled_continuous aligned_sorted.bam > var.vcf

I want to do the same for GATK's HaplotypeCaller.

Thanks in advance,
Alon

Answer 1

[User 59]

Use MuTect if you're insistent on using something aligned with the GATK suite. HaploType caller isn't (AFAIK) designed with cancer calling in mind. FreeBayes is an excellent choice for this however.

[alons]

Daniel Swan, thank you! I will look into it. Actually i'm not very insistent on GATK, if you know other variant callers that are suitable for my purpose i'd love to hear about them.

[User 59]

You're using SureCall from Agilent - is this a SureSelect or Haloplex panel? If it's Haloplex make sure you're not removing duplicates from the data, because this will ruin your chances of detecting a variant.

[alons]

I'm using SureSelect with removing duplicates. Actually i'm looking to use SureCall as more of a validation tool, that's why i'm interested in different variant callers.