somatic CNV pipeline segmentation with custom het list?

Follow

Qing Zhang

• September 07, 2021 15:31

Hi,

I want to get allelic copy ratio for each segment with my customized hets list (we have a slightly different way to define "heterozygous in normal" from GATK's), like Allelic Capseg does.

It seems that GATK ModelSegments outputs hets and allelic segments with a single command. Is it possible to only run segmentation with preselected hets?

Thanks!

0

• 

  Pamela Bretscher

  • September 09, 2021 15:54

  Hi Qing Zhang,

  As far as I know, there isn't a way to run ModelSegments with your own het file (i.e. without the genotyping step). However, you can tweak parameters such as minimum-total-allele-count, genotyping-homozygous-log-ratio-threshold, and genotyping-homozygous-log-ratio-threshold when running ModelSegments to change the requirements and way that hets are defined. Descriptions of these options can be found in the ModelSegments Tool Documentation. Do you think that adjusting these parameters would allow you to get closer to your intended set of hets?

  Kind regards,

  Pamela

  0

  Comment actions Permalink
• 

  Qing Zhang

  • September 09, 2021 20:03

  Thanks Pamela.

  After some discussion with Sam on slack, I think we are going to do this by replacing "allelic-counts" with custom hets genotypes by ourselves, set all filtering criteria to be as lenient as possible, e.g. setting minimum-total-allele-count-case minimum-total-allele-count-normal to be ~10, and increasing genotyping-homozygous-log-ratio-threshold to be 0. However, I have not got around to test this idea — I will let you know if this works as we’d expect!

  0

  Comment actions Permalink
• 

  Pamela Bretscher

  • September 09, 2021 20:07

  Hi Qing Zhang,

  Thank you for posting this potential solution here as it may help other users in the same situation and please update with your results!

  Kind regards,

  Pamela

  0

  Comment actions Permalink

Please sign in to leave a comment.