Allelic Depth Ratio


I just started to use GATK. For practice I started to work on NA12892 demo data on GATK FTP site. I called the variants on bam file and generate VCF data. Then visualize the data on Golden Helix software.

I noticed that in many locus, the allelic frequency (ratio of AD to DP) is generally about 1 (homozygote), 0.5 (heterozygote), or 0 (homozygote). However, in some regions it is as low as 0.1-0.2. For example, while DP was 700, AD was 100.

What does it mean? Why, AD is not 0.5 or just 0? How can "allelic frequeny in some locus of one sample" be 0.125?

Thank you.

P.S. Sorry if it is silly question.

Best Answers


  • CanHCanH Member

    [...] You can adjust the confidence thresholds if you want to reject these calls earlier in the process.

    To adjust the confidence thresholds, I have to use -stand_call_conf and -stand_emit_conf arguments in UnifiedGenotyper tool, right?

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