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1. Deprecated_exome-vc-pipeline Deprecated_exome-vc-pipeline Public

   Exome variant calling pipeline using BWA mem, Stampy, GATK plus samtools etc.

   Shell

2. Exome-vc-pipelineV2 Exome-vc-pipelineV2 Public

   Exome pipeline version 2 using GATK 3.0

   Shell 1

3. VariantFilterScripts VariantFilterScripts Public

   Python 3

4. FilteredVariantAnnotation FilteredVariantAnnotation Public

   Files for annotating tsv containing filtered variants

   Shell

5. Exome-vc-pipeline-V3 Exome-vc-pipeline-V3 Public

   This is essentially a variation of V2, but in this case the pipeline is desgined to work on CentOS systems with out a scheduler capable of arrays and holds as per qsub.

   Shell 1

6. My_pipelines My_pipelines Public