@transform(callSNPs, suffix('.SNP.vcf'),
            ['.SNP.filtered.vcf', '.SNP.filtered.vcf.idx', '.filterSNPs.Success'])
def filterSNPs(inputs, outputs):
    """
    Use GATK VariantFiltration to filter raw SNP calls.
    """
    input_vcf, _idx, _success = inputs
    output_vcf, _idxout, flag_file = outputs
    logFile = mkLogFile(logDir, input_vcf, '.filterSNPs.log')
    print "filtering SNPs from %s" % input_vcf
    runStageCheck('filterSNPs', flag_file, ref_files['fasta_reference'], input_vcf, logFile, output_vcf)
dataset/ETHPy150Open vlsci/variant_calling_pipeline/pipeline.py/filterSNPs/original