Tagged with #heterzygosity
0 documentation articles | 0 announcements | 2 forum discussions


No posts found with the requested search criteria.
No posts found with the requested search criteria.
Comments (4)

Hi to all,

I am calling variants in a pooled sample of 3 human samples, using UnifiedGenotyper and a ploidy of 6 and I was wondering if it is necessary to adjust the heterozygosity rate (--heterozygosity) to be 0.003 instead of the default of 0.001, or if the model used in the pooled sample calling already takes this into account.Thanks a lot,

Jaime

Comments (1)

I have an inbred mouse strain that I am sequencing and there should be little to NO heterozygosity. Yet with the default settings of UGT -heterozygosity (which is 0.001) many homs are being called as hets. When 230/250 reads are alternate and 20/250 are reference, it calls a het, even though it should be homozygous alternate.

What do you recommendations for this setting for inbred animals?

thanks, GATK is great!

Vivek