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ref/alt allele count from filtered reads

eranmickeranmick Posts: 1Member

Hi,

I was wondering whether there was any way to obtain the ref/alt allele count based only on filtered reads in UnifiedGenotyper? The output format allows you to see how many reads were filtered in total based on the difference between INFO and FORMAT DP, but not how filtering affects the AD.
I understand the logic behind this standard output format, but what approach could I take to get the post-filtering AD?

Many thanks.

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