a VCF file (dbSNP, hapmap) vcfPytools.py annotate --in=$input1 #if $annotation_options.annotate == "dbsnp" --dbsnp=$input2 #elif $annotation_options.annotate == "hapmap" --hapmap=$input2 #end if --out=$output1 dbSNP vcf file hapmap vcf file

**What it does** This tool uses vcfPytools_' annotate command annotate a VCF file .. _vcfPytools: https://github.com/AlistairNWard/vcfPytools Currently, either a hapmap or a dbsnp file should be provided, not both. dbSNP option will annotate the VCF file with dbSNP rsid values. The input dbSNP file must also be in VCF v4.0 format. Only dbSNP entries with VC=SNP are included. hapmap option will annotate the VCF file info string to include HM3 if the record is included hapmap. If the ref/alt values do not match the hapmap file, the info string will be populated with HM3A.