Overview

This repository contains data indexes 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 v0.1.4.

Datasets

Panel Data

State

• grz-cli validate: PASS
• QC pipeline: UNKNOWN

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

• grz-cli validate: PASS
• QC pipeline: FAIL (Low coverage of data)

Origin

Garvan NA12878 HG001 HiSeq Exome

WGS Trio Data

State

• grz-cli validate: FAIL
• QC pipeline: UNKNOWN

Origin

• Father: HG003 (NA24149)
• Mother: HG004 (NA24143)
• Son: HG002 (NA24385)

WGS Tumor+Germline Data

State

• grz-cli validate: PASS
• QC pipeline: UNKNOWN

Origin

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

WGS Long Read Data

State

• grz-cli validate: FAIL
• QC pipeline: UNKNOWN

Origin

NA24385 Long Read Genome Sequencing