WorkFlow_fastq2vcf

A Cromwell workflow to call and filter variants from sequencing data.

1. QC on samples raw sequencing data

java -Dconfig.file=sge.config -Xms32G -Xmx32G -jar cromwell.jar run fastQC.wdl --inputs fastQC.inputs.json > fastQC.log

2. Align samples raw sequencing data (fastq -> bam)

java -Dconfig.file=sge.config -Xms32G -Xmx32G -jar cromwell.jar run alignment_WGS.wdl --inputs alignment_WGS.inputs.json > alignment_WGS.log

3. Call variants (bam -> vcf)

java -Dconfig.file=sge.config -Xms32G -Xmx32G -jar cromwell.jar run VariantDiscovery.wdl --inputs VariantDiscovery.inputs.json > VariantDiscovery.log

4. Filter variants

java -Dconfig.file=sge.config -Xms8G -Xmx8G -jar cromwell.jar run VariantFiltering.wdl --inputs VariantFiltering.inputs.json > VariantFiltering.log