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VCF2TileDBException : Incorrect cell order found

Continued from : https://gatkforums.broadinstitute.org/gatk/discussion/11437/task-jointgenotyping-importgvcfs-failed-with-message-10-failed-to-copy-files

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:
https://console.cloud.google.com/storage/browser/genomics-public-data/gatk-examples/example1/NA19913/

The reference data is from:
https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/

The pipelines are:
https://github.com/gatk-workflows/gatk4-data-processing
https://github.com/gatk-workflows/gatk4-germline-snps-indels

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.

Issue · Github
by shlee

Issue Number
3086
State
closed
Last Updated
Assignee
Array
Closed By
sooheelee

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