26 <!-- edit these options to reflect sets of normal you have available. The values must name files within the directories specified in data_table_conf.xml file -->
27 <param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples, for hg18 54 genomes will be used.">
35 <param name="thresholdhc" type="text" value="10" label="High Confidence Threshold: Label a somatic variant as high-confidence if locus was fully called in at least this many normal genomes" help="Please adjust according to number of normals used and desired stringency. "/>
42 <data format="tabular" name="output_filtered_highconf" label="${fname} High Confidence Filtered variants for ${tool.name} on ${on_string}" from_work_dir="output_filtered_highconf.tsv"/>
50 The tool will also output how often the variant was found in one or both alleles (01 or 11), and distinguish between a variant not being present in the normal (00)
57 This program takes as input a list of variants as produced by the ListVariants tool, or the vcf-to-LV preprocessing tool. Input must be a tab-separated file of the following format::
73 2) Filtered version of output 1, variants are removed when present in at least *threshold* of the background normal genomes (default: 1) (filters on column 9 of output file)
75 3) High Confidence filtered version of output 2. Of all the variants labelled somatic, filter out any variants not fully called in at least *high confidence threshold* normals. (filter on column 11 of output file)
