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,