sauerkraut

List of test data

• reference_hg38: Reference fasta file, index files, and resource files according to human genome assembly hg38.
• reference_hg19: Reference fasta file, index files, and resource files according to human genome assembly hg19.
• germlineWGS_hg38: Germline whole genome sequence (WGS) data mapped on hg38.
• somaticWGS_hg38: Somatic WGS data mapped on hg38.
• somaticCNV_hg19: Somatic copy number variation (CNV) data mapped on hg19.
• germlineRNA_hg19: Germline RNA-Seq data mapped on hg19.

Steps to create test data

Step 1. Install cwltool

You can install cwltool by executing the following commands:

$ cd /path/to/working/directory/
$ python -m venv cwlenv
$ . cwlenv/bin/activate
$ python -m pip install --upgrade pip

Please confirm the cwltool version:

$ cwltool --version
/path/to/working/directory/cwlenv/bin/cwltool 3.1.20230201224320

Step 2. Download and create test data related to reference_hg38

Download reference file, index files, and resource files from the URLs listed in reference_hg38.download_links.txt by executing the following commnd:

$ cd /path/to/working/directory/
$ OUTDIR=reference_hg38 ; mkdir -p $OUTDIR ; for url in `cat sauerkraut/download_links/reference_hg38.download_links.txt` ; do echo $url ; file=`basename $url` ; if [ ! -f ${OUTDIR}/$file ] ; then wget $url -O ${OUTDIR}/$file ; fi ; done

reference_hg19

germlineWGS_hg38

somaticWGS_hg38

somaticSNV_hg19

germlineRNA_hg19