Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
VCF2TileDBException : Incorrect cell order found
I am processing an example fastq file, using the best practice pipeline, but getting this error:
terminate called after throwing an instance of 'VCF2TileDBException' what(): VCF2TileDBException : Incorrect cell order found - cells must be in column major order. Previous cell: [ 0, 58999902 ] current cell: [ 0, 58999902 ].
The fastq files are ERR250256 from:
The reference data is from:
I have made some small modifications to the pipelines, necessary to have them run on my backend. These are reflected in the scripts below.
I have attached a bash script replicating the cromwell pipeline, all the above linked files should be in the cwd.