diff --git a/cgatpipelines/tasks/exome.py b/cgatpipelines/tasks/exome.py index edee873f..e9521ba2 100644 --- a/cgatpipelines/tasks/exome.py +++ b/cgatpipelines/tasks/exome.py @@ -337,21 +337,6 @@ def vcfToTable(infile, outfile, genome, columns, gatkmem): ############################################################################## -def snpSift(infile, outfile, vcf, bgzip=True, memory="6G"): - '''Annotate VCF with other VCF''' - job_memory=memory - statement = '''SnpSift annotate - -Xmx%(job_memory)s %(vcf)s - %(infile)s > %(outfile)s 2> %(outfile)s.log;''' - if bgzip: - statement += '''bgzip %(outfile)s; - tabix -p vcf %(outfile)s.gz''' - P.run(statement) - - -############################################################################## - - def selectVariants(infile, outfile, genome, select): '''Filter de novo variants based on provided expression''' statement = '''gatk SelectVariants