1. findGenes : Parses the Genetic Association Database (from NIH) into an annotated 'genes of interest' interval_list file.
2. sortGenesByCoverage : combines the interval_list of the genes of interest with the report from GATK's DepthOfCoverage, generating an annotated interval_list with total and average coverages on each gene.
3. hasTheseTargets : Give it a list of targets (example: exon targets) and any interval_list (example: genes of interest) and it will generate an annotated interval_list of all the exons that are contained in the list of genes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5894 348d0f76-0448-11de-a6fe-93d51630548a
added the ccs datasets to the pbCalling pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5233 348d0f76-0448-11de-a6fe-93d51630548a
Regular updates to the pbCalling pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5232 348d0f76-0448-11de-a6fe-93d51630548a
remapAmplicons.lua takes a sam file with reads aligned to amplicon references, a reference genome , and an amplicon reference mapping table, and rewrites the sam file with mappings to the reference sequence.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5230 348d0f76-0448-11de-a6fe-93d51630548a
ps: this utility is similar to -im on GATK, but for queue scripts we need the intervals file fixed before we can run Unified Genotyper because of scatter-gather.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5117 348d0f76-0448-11de-a6fe-93d51630548a
carneiro