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are there Alternatives for JointCalling (Germline variant calling) for <50 samples?

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    Jason Cerrato

    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

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    Samuel Terkper Ahuno

    thanks Jason! I'll give it a try.

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    Samuel Terkper Ahuno

    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`

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    Jason Cerrato

    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

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