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PublicPairedSingleSampleWf_170412.inputs.json Update GOTC single-sample workflow to functional equivalence version Apr 11, 2017
PublicPairedSingleSampleWf_170412.md Update supported GOTC single-sample and add pipeline documentation Apr 11, 2017
PublicPairedSingleSampleWf_170412.options.json Update GOTC single-sample workflow to functional equivalence version Apr 11, 2017
PublicPairedSingleSampleWf_170412.wdl Update GOTC single-sample workflow to functional equivalence version Apr 11, 2017
README.md Update README.md Apr 21, 2017

README.md

Content overview

This directory contains the following WDL scripts used in production at the Broad Institute. Old versions are stored in the archive directory. Versions are distinguished with a datestamp (format: YYMMDD). Each WDL script is accompanied by a JSON file of example inputs bearing the same name, with the .inputs.json extension instead of .wdl, as well as a JSON file of example options with the .options.json extension.

Important limitations

These scripts are provided "as-is", without any guarantees as to performance or results. It is the responsibility of the user to test these scripts fully before running them in production.

Many parameters and implementation decisions are optimized for our use of the Google Cloud Platform. In some cases (such as dynamic filename modifications and extension swapping using the sub() function) the scripts may need to be modified in order to be run successfully on a different platform.

Inventory of scripts

PublicPairedSingleSampleWf-<datestamp>.wdl

This WDL pipeline implements data pre-processing and initial variant calling (GVCF generation) according to the GATK Best Practices for germline SNP and Indel discovery in human whole-genome sequencing (WGS) data.