Support #23
Updated by Gerrit Botha about 7 years ago
We need to test [this workflow](http://edicogenome.com/pipelines/gatk-best-practices-workflow-on-dragen).
The sample data for the child of a GiaB trio NA12878 has been shared with Jon. The WGS sequencing has been done on a Illumina HiSeq 2000 at X50. 100bp paired end.
* The forward reads can be downloaded [here](ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_1.fastq.gz)
* The reverse reads can be downloaded [here](ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_2.fastq.gz) [here](ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_1.fastq.gz)
There is a local copy of the reads at CHPC as well, but the permissions to where it is stored just need to be opened.
Once we have done testing we might need to see if we can also get hold of a publicly available HiSeq X Ten sample (150bp) just to see how much need to be adjusted for the alignment step.
The sample data for the child of a GiaB trio NA12878 has been shared with Jon. The WGS sequencing has been done on a Illumina HiSeq 2000 at X50. 100bp paired end.
* The forward reads can be downloaded [here](ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_1.fastq.gz)
* The reverse reads can be downloaded [here](ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_2.fastq.gz) [here](ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_1.fastq.gz)
There is a local copy of the reads at CHPC as well, but the permissions to where it is stored just need to be opened.
Once we have done testing we might need to see if we can also get hold of a publicly available HiSeq X Ten sample (150bp) just to see how much need to be adjusted for the alignment step.