Takes a high quality snp vcf, bam, and a vcf to evaluate for sens/spec

This DNA Nexus App wraps a standalone python version of the evaluator that can be used without DNANexus

usage: standalone_accuracy_evaluator.py [-h] [--bed_file BED_FILE]
[--bam_file BAM_FILE]
[--ref_vcf REF_VCF]
[--eval_vcf EVAL_VCF]
[--ref_fasta REF_FASTA]

Take in a high quality snp/indel set and evaluate a call set for concordance

optional arguments:
-h, --help show this help message and exit
--bed_file BED_FILE bed file to limit comparisons to certain regions

required arguments:
--bam_file BAM_FILE bam file to use to get readcounts for missing sites
--ref_vcf REF_VCF file of SNPs or INDELs you know to be true in your callset
--eval_vcf EVAL_VCF file of SNPs and/or INDELs you want to compare to the known true callset
--ref_fasta REF_FASTA reference fasta used to call the bam

This is the source code for an app that runs on the DNAnexus Platform. For more information about how to run or modify it, see https://wiki.dnanexus.com/.

Evaluates any vcf generated from data that has a trusted set of snps for accuracy, and generates lists of missed variants