Description Usage Arguments Examples
Parse panel of normal variants to standardise output across callers
1 | parse_pon(path_to_pon, caller)
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path_to_pon |
link to panel of normal file created with GATK3 VariantsToTable using at least |
caller |
one of 'varscan', 'mutect' or 'vardict'. This field is needed to parse the variant allele frequency field which is recorded differently across callers. |
1 2 3 | path_to_pon = "varscan_calls/PON_varscan_target_regions.table"
parse_varscan <- parse_pon(path_to_pon,'varscan')
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