We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Questions about --sample_ploidy, --indel_heterozygosity, and --heterozygosity

skblazerskblazer Member
edited August 2012 in Ask the GATK team

Hi,

I worked on a uncommon species, of which reference is organized within scaffolds but chromosomes?
Do I still need to set --sample_ploidy?

For --sample_ploidy and --indel_heterozygosity,
If I can use the default settings in case of unknown heterozygosity for the population I'm interested with. If I found there are significantly higher heterozygosity in the result, do I need to re-call the variants by setting the new heterozygosity?

Best,
SK

Best Answer

  • delangeldelangel Broad Institute ✭✭
    Accepted Answer

    If your underlying organism is still diploid I wouldn't change the -ploidy argument. This is intended to specify how many homologous chromosomes you have per sample (e.g. 2 for humans).
    If you have enough depth the heterozygosity arguments will have very little effect and you may only see a difference in marginal calls close to the calling boundary.

Answers

  • delangeldelangel Broad InstituteMember ✭✭
    Accepted Answer

    If your underlying organism is still diploid I wouldn't change the -ploidy argument. This is intended to specify how many homologous chromosomes you have per sample (e.g. 2 for humans).
    If you have enough depth the heterozygosity arguments will have very little effect and you may only see a difference in marginal calls close to the calling boundary.

  • skblazerskblazer Member

    Many thanks for the response.

Sign In or Register to comment.