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add additional BED interval information #46

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add additional BED interval information #46

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add additional BED interval information
Sep 24, 2019
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Update 03.methods.md
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3 changes: 2 additions & 1 deletion content/03.methods.md
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Expand Up @@ -77,7 +77,8 @@ We required at least 60% of RNA-Seq reads mapped to the human reference or sampl
#### SNV and INDEL calling

We used four variant callers to call SNVs and INDELS from targeted DNA panel, WXS, and WGS data: Strelka2, Mutect2, Lancet, and VarDict.
The same input interval BED files were used for both panel and WXS data.
The same input interval BED files were used for both panel and WXS data and these were padded by 100 bp for all variant calling algorithm runs.
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Does this mean +100bp was added on both sides of the range? Or +50bp on each side? Also what was the reasoning behind this padding? Did this come from a recommendation from one of the callers?

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100bp on each side. This did come from recommendations from the callers, with the exception of lancet - we tested multiple and took the best for precision and performance.

The BED files for WGS were not padded for Mutect2 and Strelka2 runs, were padded by 300 bp for Lancet, and by 100 bp for VarDict.
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Why were these padding window numbers chosen? Also, I have the same question about how this window padding is reported.

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whoops, answered this above. Does that help?

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Yes! It does. Can you add this information in the text?

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done!

Strelka2 [@doi:10/gdwrp4] v2.9.3 was run using default parameters on human genome reference hg38, canonical chromosomes only (chr1-22, X,Y,M), as recommended by the authors.
The final Strelka2 VCF was filtered for PASS variants.
Mutect2 from GATK v4.1.1.0 was run following Broad best practices outlined from their Workflow Description Language (WDL) [@url:https://github.com/broadinstitute/gatk/blob/4.1.1.0/scripts/mutect2_wdl/mutect2.wdl].
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