Question: How to call low frequency snp/indel with GATK's HC/UG
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gravatar for polangxin
6.4 years ago by
polangxin80
United States
polangxin80 wrote:

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 cant do with HC.

THANKS!

snp gatk indel • 2.0k views
ADD COMMENTlink modified 5.6 years ago by jingyc010 • written 6.4 years ago by polangxin80
0
gravatar for jingyc01
5.6 years ago by
jingyc010
jingyc010 wrote:

hello 

      have you sovle your problem?

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

ADD COMMENTlink written 5.6 years ago by jingyc010
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