#1536 closed task (fixed)
Implement variant calling for paired WGS
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | major | Milestone: | Reggie v4.50 |
Component: | net.sf.basedb.reggie | Keywords: | |
Cc: |
Description
The plan is to use GATK Mutect2 (https://gatk.broadinstitute.org/hc/en-us/articles/13832710384155-Mutect2) for variant calling on tumor/normal pairs.
The general workflow is outlined here: https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels-
Before we can implement the whole pipeline there are a number of things that need to be prepared:
- Our BAM files are not fully "analysis-ready" since GATK recommends that a "base quality recalibration" step is performed (https://gatk.broadinstitute.org/hc/en-us/articles/360035535912). We have tested this and noticed that this step increases the size of the BAM file with about 2x. So we will keep our BAM files as the are and run the recalibration step as part of the variant calling (it should take about 3-4 hours for a pair of BAMs with 30x coverage).
- Several steps in the pipeline requires a VCF (one or more) with information about know variants. The suggestion is to use for example, GnomAD or dbSNP. But they will need to be properly prepared and maybe filtered before use.
- A "panel-of-normals" data set need to be created by running Mutect2 in tumor-only mode on a number of normal samples and then building a combined VCF from that information (https://gatk.broadinstitute.org/hc/en-us/articles/13832769396635-CreateSomaticPanelOfNormals-BETA-). Since we have more than one library preparation protocol we should create separate sets of "panel-of-normals" for each protocol.
Change History (34)
comment:1 by , 12 months ago
comment:2 by , 12 months ago
Milestone: | Reggie v4.x → Reggie v4.50 |
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Status: | new → assigned |
comment:33 by , 12 months ago
Resolution: | → fixed |
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Status: | assigned → closed |
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