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I have tumor only calls with Mutect and would like to filter them further. My first question is, if CNNScoreVariants applicable to this? If so, I can't get it work. The command line I am using (tried both 1D and 2D models) (also tried different batch sizes in 2D model):
/GenomeAnalysisTk/22.214.171.124/gatk CNNScoreVariants -V /path/to/input_somatic_twicefiltered.vcf.gz -R /ref/hg19/Homo_sapiens_assembly19.fasta -O /path/to/output_annotated.vcf --intra-op-threads 20
However I am always stuck at this level and no progress (for days)
13:00:07.286 INFO CNNScoreVariants - Initializing engine 13:00:14.027 INFO FeatureManager - Using codec VCFCodec to read file 13:00:14.661 INFO CNNScoreVariants - Done initializing engine
I am only providing 1 sample here. Do I supposed to provide a batch? Or what else I could be doing wrong?