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add additional BED interval information #46
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new info I learned while preparing V5 data
cansavvy
reviewed
Sep 24, 2019
content/03.methods.md
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| @@ -77,7 +77,8 @@ We required at least 60% of RNA-Seq reads mapped to the human reference or sampl | |||
| #### SNV and INDEL calling | |||
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| 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.
content/03.methods.md
Outdated
| @@ -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. | |||
| 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?
updates per @cansav09
cgreene
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Sep 29, 2019
This build is based on dd26041. This commit was created by the following Travis CI build and job: https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/builds/129611183 https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/jobs/240177123 [ci skip] The full commit message that triggered this build is copied below: Merge pull request #46 from AlexsLemonade/update-bed-methods add additional BED interval information
cgreene
pushed a commit
that referenced
this pull request
Sep 29, 2019
This build is based on dd26041. This commit was created by the following Travis CI build and job: https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/builds/129611183 https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/jobs/240177123 [ci skip] The full commit message that triggered this build is copied below: Merge pull request #46 from AlexsLemonade/update-bed-methods add additional BED interval information
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new info I learned while preparing V5 data
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