How do I call germline variants with multiple samples -non human?
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Have not used gatk in a couple years, and I'm going around in circles here looking for what is currently recommended for generating germline variant calls for multiple non-human samples. Is there a current pipeline for that?
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just to add - I do have a reference genome, and the genome is fairly small relative to human, without as many repeat issues.
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Hi Jody Hey,
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Hi Jody Hey,
We don't have a Best Practices pipeline for this at the moment, but you can generally run our tools on non-human samples. There are many examples on the forum of people with similar use cases. For even more conversation, you can check out our legacy forum site (some of it is out of date, so keep in mind): https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/
Some aspects of GATK are meant to only work for humans, for example the SV pipeline, and the SNP and INDEL heterozygosity. But many tools are flexible, for example, HaplotypeCaller, which is our Best Practices variant caller for germline. See this document for more details: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-
Best,
Genevieve
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I am also looking into the GATK-SV tool to identify variants in non-human genomes. Is the tool still restricted to human-genome use? If yes, then would the beta tool StructuralVariationDiscoveryPipelineSpark provide a reliable alternative for a non-human genome?
Best regards
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Thanks for writing in with this question Domniki Manousi. The GATK-SV tool was built for human use, but I do know that there are some groups using it for non-human data as well. It won't work out of the box - you'll need to do some modifications of the workflow, there are definitely some points where the chromosome names are hard coded.
We no longer maintain the spark pipeline, so I wouldn't recommend trying it out at this point.
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