unified genotyper for pooled data > Allele Number
I want to anaylze pooled sequencing data, and i found out gatk has an option for these in UG: --ploidy.
So, i gave an option --ploidy 100, cuz this pool contains 50 individuals.
Also i added one more option -glm GENERALPLOIDYINDEL for indel calling.
After, i am looking at a raw vcf file, and i dont understand it.
it's because all the AN is just 100.
So, AF, AC and MLEAF values are also weird.
have one more question,
i want to run a few more steps to trim a raw vcf file, using Select Variants and Variant Filtration.
But they dont seem to have any option for ploidy. Then, how can i proceed while not loosing any information about ploidy?
just dont put options like -selectType?
i hope you guys have solutions for my problem.
Thank you, in advance.