github.com/TrinityCTAT/ctat-mutations-benchmarking/ctat_mutations_benchmarking

Automatic Tools and Workflows
1

RNA-seq Variant Calling Benchmarking

Benchmarking using a truth-set VCF


    ../BENCHMARK_variant_calling.py \
        --pred_vcf methodA.vcf [methodB.vcf methodC.vcf ...] \
        --truth_vcf truth.vcf \
        --pred_bam rnaseq_alignments.bam \
        --rna_editing rnaediting.vcf.gz \
        --output_dir "bmark.outdir"

     and optionally:
         [ --restrict_regions_bed trusted_regions.bed ] \
         [ --snvs_only or --indels_only ]

Separately evaluate SNVs or InD

This is a companion discussion topic for the original entry at github.com/TrinityCTAT/ctat-mutations-benchmarking/ctat_mutations_benchmarking