germline mutation calling using per-sample module
Answered
Hi,I'm a newer to gatk. I try to use gatk to call germline mutation from my tumor data. I see that there are to modules, per-sample and joint genotyping, I wonder that per sample module compatible to hg19 reference genome? the attached picture shows that per sample module only support hg38. Hope your response!
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Thank you for your post, chenglei! I want to let you know we have received your question and will be moving it to the Community Discussions -> Documentation Questions topic, as the Germline topic is for reporting bugs and issues with GATK.
We'll get back to you if we have any updates or follow up questions. Please see our Support Policy for more details about how we prioritize responding to questions.
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Hi chenglei,
The link you are showing here is the best practices implementation in a pipeline easily runnable on Terra.
- GATK Best Practices Germline short variant discovery: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-
- GATK Best Practices for Germline SNPs & Indels on Terra for hg38: https://app.terra.bio/#workspaces/help-gatk/Germline-SNPs-Indels-GATK4-hg38
You can easily run the germline short variant discovery best practices pipeline with hg19. You can follow the instructions on the best practices page on your own and use the hg19 reference, or you can edit the best practices WDL workflow on Terra to use the hg19 reference. Either way, you should be able to run it just fine and get good results.
Please let us know if you have any other GATK questions.
Best,
Genevieve
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