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1. CIDR_WES CIDR_WES Public

   CIDR's production pipeline for WES and other targeted DNA sequencing projects.

   Shell

2. CIDR_SEQ_CAPTURE_JOINT_CALL CIDR_SEQ_CAPTURE_JOINT_CALL Public

   CIDR exome and targeted resequencing joint calling/filtering pipeline

   Shell

3. CIDR_SOMATIC_WES_PIPELINES CIDR_SOMATIC_WES_PIPELINES Public

   currently for paired tumor - normal WES samples processed with TWIST UMIs

   Shell 1

4. CIDR_EXOME_MITO CIDR_EXOME_MITO Public

   stop gap exome pipeline ported over from clinical stand-alone pipeline

   Perl

5. CIDR_DATA_ARCHIVING CIDR_DATA_ARCHIVING Public

   Shell

6. DEMUX_BCL2FQ DEMUX_BCL2FQ Public

   Brian Craig's scripts for lab managers to use for submitting ilmn bcl2fastq jobs to sge

   Shell