Attention:
The frontline support team will be offline as we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and available to answer questions on the forum on March 25th 2019.

GenotypeGVFs, -ploidy

manolismanolis Member ✭✭
edited January 14 in Ask the GATK team

GATK 4.0.11.0, human WES

Hi,

I'm using HaplotypeCaller with the -ploidy option for the sex chromosomes:

Male: chr1-22 = ploidy 2
Male: chrX,Y = ploidy 1

Female: chr1-22,X = ploidy 2

With the MergeVcfs I merge the two male gvcfs to one and then I join my cohort gvcfs (males and females samples) with GenomicsDBImport and at the end I'm going to use GenotypeGVCFs.

I cann't figure out how to calculate the ploidy value to set up with GenotypeGVCFs. What is the meaning of "pool" in my case? My male gvcfs have a mixed ploidy. I have to change strategy? I have 50 male and 55 female samples.

Many thanks

> ----------------------------
> --sample_ploidy / -ploidy
> Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
> Sample ploidy - equivalent to number of chromosome copies per pool. For pooled experiments this should be set to the number of samples in pool multiplied by individual sample ploidy.
> ----------------------------
Post edited by manolis on

Best Answer

Answers

  • manolismanolis Member ✭✭
    edited January 15

    Hi @AdelaideR

    I had seen the special note, just I made some confusion reading the comment about "--sample_ploidy / -ploidy".

    Many thanks

Sign In or Register to comment.