Quantcast
Channel: Post Feed
Viewing all articles
Browse latest Browse all 3147

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

$
0
0

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!


Viewing all articles
Browse latest Browse all 3147

Trending Articles