Hi I have several variants (especially those with almost hom-alt allele) that have different allele fraction estimates from DP4 and the AF= tag. for example
DP=4088;AF=0.872798;SB=171;DP4=9,33,3329,685
Here from DP4, the AF can be estimated to be about 0.98189 which is very different from what is published in the AF= tag. Could you please explain?
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Hi I have several variants (especially those with almost hom-alt allele)
that have different allele fraction estimates from DP4 and the AF= tag. for
example
DP=4088;AF=0.872798;SB=171;DP4=9,33,3329,685
Here from DP4, the AF can be estimated to be about 0.98189 which is very
different from what is published in the AF= tag. Could you please explain?
Hi I have several variants (especially those with almost hom-alt allele) that have different allele fraction estimates from DP4 and the AF= tag. for example
DP=4088;AF=0.872798;SB=171;DP4=9,33,3329,685
Here from DP4, the AF can be estimated to be about 0.98189 which is very different from what is published in the AF= tag. Could you please explain?
Hello,
DP4 only lists the reference and variant base counts. There are usually
other bases present as well, which are taken into account for computing AF.
Hoping this explains the discrepancy,
Andreas
On 26 October 2017 at 04:58, siva siva80@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC