Map reads to a reference with alternate contigs like GRCH38 using GATK4
Hi,
We are in process of shifting our in-house pipeline for exome sequencing data analysis and variant calling based on GRCh38 and we would like to do alt-aware alignment for the same. I have gone through the below article which was written for GATK3 but it would be really helpful if someone can let me know whether I can use the same protocol for GATK4.
https://gatk.broadinstitute.org/hc/en-us/articles/360037498992
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Hi neethukrishna Kausthubham, we are still in the process of updating that article. You should be able to test out the main steps, then adapt the pipeline with GATK4 tools instead of GATK3 tools. Many of the tools have the same name, so it may be easy to adapt.
You can also see this article for the Germline short variant discovery (SNPs + Indels) Best Practices, as well as Data pre-processing for variant discovery Best Practices. These are up to date with GATK4 so they have the correct command usage.
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Genevieve Brandt (she/her), thank you for the reply. I was just going through the alt-aware alignment and I am not very clear how to deal with the downstream analysis. But gradually I may be able to figure this out.
It would be great if anyone can address the following concern.
1) In a clinical context, if we use the reference which contains only the primary assembly of GRCH38 then will it make a huge impact on the downstream analysis? -
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