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Error while running gatk GenomicsDBImport
I am trying to create a panelofnormals file using this tutorial: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_CreateSomaticPanelOfNormals.php
I have an interval file that looks like this:
I am getting an error like this:
htsjdk.tribble.TribbleException: Invalid interval record contains 1 fields: chr1:1-248956422, for input source: /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/my.interval_list
I tried changing my interval files to something like this (with tabs):
chr1 1 248956422
chr2 1 242193529
chr3 1 198295559
chr4 1 190214555
chr5 1 181538259
chr6 1 170805979
chr7 1 159345973
chr8 1 145138636
chr9 1 138394717
chr10 1 133797422
But i still get an error like this:
htsjdk.tribble.TribbleException: Invalid interval record contains 3 fields: chr1 1 248956422, for input source: /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/my_new.interval_list
What do I do now to solve this?