GRZ mock submissions and GRZ JSON Editor

Overview

This repository contains GRZ mock submissions for testing purposes; additionally it offers a GRZ schema compliant json editor, which aims to facilitate the creation of json files for the clinics that participate in the Modellvorhaben.

The data indexes are taken from NIST’s Genome in a Bottle (GIAB) project. The indexes for sequences and alignments are also available at NIST GIAB FTP.

Submissions are validated using grz-cli v0.3.0.

JSON Editor

GRZ JSON Editor Schema Version 1.1.4

Datasets


Panel Data

State

Origin

Garvan NA12878 HG001 HiSeq Exome

Processing

  1. Created panel FASTQ files from panel gene list csv, .bed and .bam files.

  2. Generate Panel BED File:
    Run the script ./extract_panel_bed_file.sh to create the panel .bed file.

  3. Intersect BAM with Panel BED:
    Use bedtools intersect to filter the input .bam file with the panel .bed file:

    bedtools intersect -abam input.bam -b panel.bed > panel.bam
  4. Run convert_bam_to_fastq.sh script to convert panel bams to paired-end fastq files

    ./convert_bam_to_fastq.sh <BAM_FILE_PREFIX> <OUT_FASTQ_FILE_PREFIX>
  5. Use bedtools intersect to filter the input .vcf file with the panel .bed file

    bedtools intersect -header -a input.vcf -b panel.bed > panel.vcf

WES Tumor + Germline Data

State

Origin

Garvan NA12878 HG001 HiSeq Exome


WGS Tumor+Germline Data

State

Origin

HG008 Liss Lab BCM Illumina-WGS (2024-03-13)


WGS Trio Data

State

Origin


WGS Long Read Data

State

Origin

NA24385 Long Read Genome Sequencing