Advanced argument settings

Parameter

Description

Torrent Variant Caller arguments

Advanced arguments for Torrent Variant Caller.

Alignment arguments

Desirable alignment arguments for variant calling purpose. Realignment of the BAM file may be triggered in the plugin if the entry is different from the alignment arguments specified in the run plan.

Unify vcf arguments

Advanced manipulation of the variant calling VCF file.

SVB BED file

Full path to a previously uploaded sequence variant baseline (SVB) BED file. For example, /results/uploads/BED/65536/foo/unmerged.