are there Alternatives for JointCalling (Germline variant calling) for <50 samples?
Dear Terra,
are there any recommendations for running JointCalling for <50 samples (41)?
https://app.terra.bio/#workspaces/help-gatk/GATK4-Germline-Preprocessing-VariantCalling-JointCalling
my workflow fails with the error;
Job JointGenotyping.CheckSamplesUnique:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
stderr output;
There are fewer than 50 samples in the sample_name_map Having fewer than 50 samples means there likely isn't enough data to complete joint calling
thanks
Comments
4 comments
Hi Sam,
You can skip the joint calling workflow by running the previous workflow (Haplotypecaller) with the gVCF mode disabled. This will produce VCFs for your 41 samples instead of gVCFs that would need to be run through the joint calling workflow.
Kind regards,
Jason
thanks Jason! I'll give it a try.
Hi Jason Cerrato is there a particular reason why jointGenotyping has been capped at >= 50 samples? although, gatk best practices recommends a joint-calling for larger cohort
i still need to perform joint-calling and variant filtering. I figured out setting the attribute `sample_num_threshold` to a number less than 50 (say 40) allowed me to run workflow `JointCalling workflow`
Hi Sam,
Per your request, I'm closing out this inquiry. If you have any further questions about this, let us know and we'll get look to get them answered as soon as we are able.
Kind regards,
Jason
Please sign in to leave a comment.