Eva (Evander)
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gatk CollectVariantCallingMetrics MultiThreadedChunkBased: Unexpected exception encountered in child thread. java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
I have run the same command on two other .vcf files from different variant callers (deepvariant and gatk), with the same reference genome, bed file/targets, and dbSNP file. They have no issues and ...
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CollectGcBiasMetrics for Exome data
Dear GATK community, I want to see if there is any GC coverage bias in exome data. I am using CollectMultipleMetrics with the -PROGRAM CollectGcBiasMetrics. Is there any way to make the plot for ex...
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Does GATK4 BaseRecalibrator not understand relative paths?
I am using GATK 4.2.6.1. and for some reason GATK BaseRecalibrator is not getting my (relative) paths. It pastes them to the path all the way up to the home directory (as you can see at the end of ...