update to freebayes

Author: jodyphelan

tb-profiler

@@ -521,7 +521,7 @@ parser_sub.add_argument('--bam','-a',required=True, help='BAM file. Make sure it
 parser_sub.add_argument('--prefix','-p',default="tbprofiler",help='Sample prefix')
 parser_sub.add_argument('--outfmt',default='json',choices=["json","txt"],type=str,help="Output format")
 parser_sub.add_argument('--snps',action="store_true",help='Sample prefix')
-parser_sub.add_argument('--caller',default='bcftools',choices=["bcftools","freebayes","gatk"],type=str,help="Variant caller")
+parser_sub.add_argument('--caller',default='freebayes',choices=["bcftools","freebayes","gatk"],type=str,help="Variant caller")
 parser_sub.add_argument('--platform','-m',choices=["illumina","nanopore"],default="illumina",help='NGS Platform used to generate data')
 parser_sub.add_argument('--db',default='tbdb',help='Mutation panel name')
 parser_sub.add_argument('--external_db',type=str,help='Path to db files prefix (overrides "--db" parameter)')