Adjusting SNP frequency

0

Entering edit mode

5.6 years ago

TonyCN ▴ 60

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%.

SNP • 757 views

ADD COMMENT • link 5.6 years ago by TonyCN ▴ 60

1

Entering edit mode

I believe the term you are looking for is allelic depth/allelic ratio.

ADD REPLY • link 5.6 years ago by WouterDeCoster 47k

0

Entering edit mode

Thanks, good to know.

ADD REPLY • link 5.6 years ago by TonyCN ▴ 60

Login before adding your answer.