RNAseq short variant discovery pipline has the unused interval file

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woodword

• February 25, 2021 13:11

Today when I checked the RNAseq short variant discovery pipline (https://github.com/gatk-workflows/gatk3-4-rnaseq-germline-snps-indels/blob/master/rna-germline-variant-calling.wdl )  I found task SplitNCigarReads_GATK4 (at line 536) does not use any interval file but these is one in the function at line 541.

Is this a minor bug ?

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  Beri

  • March 03, 2021 20:14

  This is a minor bug, a fix has been merged for the latest version of the wdl (the gatk3-4 wdl is archived and is no longer being supported). 

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