Unrelated Files and Panel of Normal

For many of the CGAP Pipelines, a collection of 20 de-identified UGRP samples are used to aid in filtering common variants. This documentation page outlines how they were created.

SNV Pipeline - Unrelated RCK files

Sentieon

  1. 20 unrelated fastq files from UGRP dataset were run through the Upstream Sentieon module (v1.0.0) to generate analysis-ready bam files.

  2. The bam files were then processed using a custom module (SNV Unrelated, v1.0.0) that executes granite mpileupCounts and rckTar commands.

  3. The final file was uploaded to the CGAP Portal as: 196ef586-be28-40c5-a244-d739fd173984/GAPFIMO8Y4K1.rck.tar

GATK

  1. 20 unrelated fastq files from UGRP dataset were run through the Upstream GATK module (v1.0.0) to generate analysis-ready bam files.

  2. The bam files were then processed using a custom module (SNV Unrelated, v1.0.0) that executes granite mpileupCounts and rckTar commands.

  3. The final file was uploaded to the CGAP Portal as: eac862c0-8c87-4838-83cb-9a77412bff6f/GAPFIMO8Y4PZ.rck.tar

Somatic Sentieon - Panel of Normal (PON)

  1. 20 unrelated fastq files from UGRP dataset were run through the Upstream Sentieon module (v1.0.0) to generate analysis-ready bam files.

  2. Following this protocol from Sentieon each resulting bam file was run individually through the Somatic Sentieon Tumor Only module (v1.0.0), using GAPFI4LJRN98.vcf.gz dbSNP file for known SNPs.

  3. The 20 resulting vcf output files were merged using BCFtools (1.10.2).

  4. This file was uploaded to the CGAP Portal as: 833c91e9-a8cd-470e-8100-32b49ed14159/GAPFIV1QKYU9.vcf.gz

SV Pipeline - Manta

  1. 20 unrelated fastq files from UGRP dataset were uploaded to the (now decommissioned) cgap-wolf environment.

  2. Each of the 20 samples was run through the Upstream GATK module (v24), ending with a final bam file following workflow_gatk-ApplyBQSR.

  3. Each of the resulting final bam files was run through a proband-only Manta workflow (v2) to produce vcf files.

  4. The resulting vcf files were downloaded to a folder named unrelated, which was compressed:

tar -cvf unrelated.tar unrelated

  1. This file was uploaded to the CGAP Portal as: cd647c0c-ac11-46db-9c51-bfe238e9ac13/GAPFIH794KXC.vcf.tar

CNV Pipeline - BICseq2

  1. 20 unrelated fastq files from UGRP dataset were retrieved from Glacier Deep Archive and uploaded to the current cgap-wolf environment.

  2. Each of the 20 samples was run through the Upstream GATK module (v27), ending with a final bam file following workflow_gatk-ApplyBQSR.

  3. Each of the resulting final bam files was run through the development version of the CNV module (v1), which included only 2 steps (workflow_BICseq2_map_norm_seg and workflow_BICseq2_vcf_convert_vcf-check). This development version still included chromosomes X and Y as well, which have since been removed from the production version.

  4. The resulting vcf files were downloaded to a folder named unrelated, which was compressed:

tar -cvf unrelated.tar unrelated

  1. This file was uploaded to the CGAP Portal as: 318788cd-661f-4327-b571-d58a9b7c301e/GAPFICPW2884.vcf.tar