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Hi @Tiffany_at_Broad and @bshifaw Thanks for your helpful suggestions. It seems the "Edit Configuration" feature does not allow users to edit the WDL file. Is there another way of editing the WDL file of a method in FireCloud?
Repeating the analysis after changing platform_name from Illumina_NextSeq_500_550 to illumina in the readgroup.list file resolved the issue.
Hi @KateN Thanks for your reply. Based on your reply, I assumed that something is wrong with the ubam files, and started the analysis from scratch. I ran the method gatk/paired-fastq-to-unmapped-bam, followed by the method gatk/processing-for-varia…
Hi @bshifaw Thanks for your reply. I used a list of ubams as input like you instructed, and the workflow ran for a few hours, but then failed. There were 17 error messages similar to this: message: Task PreProcessingForVariantDiscovery_GATK4.BaseR…
Hi, I am getting incompatible contig error while trying to use these vcf files. Apparently the vcf input files have 1-22, X, Y, MT; while both my reference genome and BAM files have the following. How can I run MuTect on my BAM files? chrM, chr1, c…