How to call low frequency snp/indel with GATK's HC/UG

Question

[polangxin]

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!

[jingyc01]

Hello

Have you solved your problem?

I have a similar problem, for default condition the gatk call the frequecy of allele is?