Calculate allelic frequency from VEP output vcf file
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Entering edit mode
15 days ago

I am calculating allelic frequency for somatic variants. VEP gives a VCF file, for example that has:

9761707 G>A and outputs

DP FDP SDP SUBDP  AU  CU    GU    TU
99   0  0   0    0,0  0,0   99,99  0,0

or

121467604 T > C

DP FDP SDP SUBDP  AU    CU   GU    TU
153  0  0   0    0,0  77,79  0,0  76,76

How can I calculate the allele frequency from this information? I don't quite understand why in the first case there is nothing on AU, but the second case has something on both CU and TU. Based on my readings (recommendation here) it should be:

AU1/(AU1+GU1) for the first one and CU1/(CU1+TU1) for the second one. Yet, on the first case this would mean an allelic frequency of zero, but then why is the variant being reported at all??

Why is this?

VEP variant • 265 views
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Entering edit mode
13 days ago

Found the answer here!!

https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic

Although this leads to a strange situation in which some variants might have zero for allele frequency, which has been commented on before: https://github.com/Illumina/strelka/issues/65

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