Hi all,
I'm really looking for some help here. Again, my usual disclaimer of being neither a biologist or bioinformatician, so I apologise in advance if I mess up all of my terminologies.
I am using GenomeAnalysisTK to perform SNP calling, or whatever the correct noun is which results in a VCF file. This is great. But, I have been told I need to adjust the allelic depth/allelic ratio sensitivity as low a theoretically possible (0.1% is what I am after).
Is this possible with GenomeAnalysisTK? If not, is this possible with any other software that produces a .vcf file? That part is essential, I am a software engineer, I can write all of the end-engine but I need that .vcf file and it needs to have been the result of a very sensitive SNP calling process.
Many thanks in advance.
EDIT After digging, I believe what I want to do is filter by setting a minimum Allele Frequency to 0.1%.
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I believe the term you are looking for is allelic depth/allelic ratio.
Thanks, good to know.