If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
Task JointGenotyping.ImportGVCFs failed with message 10: failed to copy files
Task JointGenotyping.ImportGVCFs failed on joint discovery of 34 exome samples:
When I look into the stderr.log file:
08:33:54.012 INFO GenomicsDBImport - Starting batch input file preload
08:33:59.013 INFO GenomicsDBImport - Finished batch preload
08:33:59.013 INFO GenomicsDBImport - Importing batch 1 with 34 samples
terminate called after throwing an instance of 'VCF2TileDBException'
what(): VCF2TileDBException : Incorrect cell order found - cells must be in column major order. Previous cell: [ 20, 664149855 ] current cell: [ 20, 664149855 ].
The most likely cause is unexpected data in the input file:
(a) A VCF file has two lines with the same genomic position
(b) An unsorted CSV file
(c) Malformed VCF file (or malformed index)
See point 2 at: https://github.com/Intel-HLS/GenomicsDB/wiki/Importing-VCF-data-into-GenomicsDB#organizing-your-data
GVCFs were called with haplotypecaller-gvcf-gatk4 (all done with workspace: Germline-SNPs-Indels-GATK4-hg38)
What can I do to fix this error?