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!
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!