How to call low frequency snp/indel with GATK's HC/UG
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7.9 years ago
polangxin ▴ 80

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!

indel snp gatk • 2.4k views
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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?

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