How to call low frequency snp/indel with GATK's HC/UG
I want to call snp/indel with low frequency, like DP=100, ALT=10.
how to set HC/UG ?
with UG, I run with:
--min_indel_count_for_genotyping 2
--min_indel_fraction_per_sample 0.05
get a nice result, but I can't do with HC.
THANKS!
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polangxin •
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Hello
Have you solved your problem?
I have a similar problem, for default condition the gatk call the frequecy of allele is?