Last updated
Last updated
Outlined below are the steps taken to create a raw vcf file from paired end raw FASTQ files. This was done for each sequenced accession so a HTCondor DAG Workflow was written to streamline the processing of those ~200 accessions. While some cpu and memory parameters have been included within the example steps below those parameters varied from sample to sample and the workflow has been honed to accomodate that variation. This pipeline is subject to modification based on software updates and changes to software best practices.
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Above this point is the workflow for the creation of the gVCF files for this project. The following additional steps were used to create the Hapmap file
NOTE: This project has 363 gvcfs: multiple instances of CombineGVCFs, with unique subsets of gvcf files, were run in parallel to speed up this step below are examples