[svtoolkit-help] user filtering

[Wenhua W. <wen...@ot...>]

Dear Bob,


I have been through the filtering discussions briefly. I have a couple of questions re user intervention/filtering mentioned at your tutorial July 2013. I assume the user filtering is not incorporated in the discovery.sh or genotype.sh in the installtest directory (version 2.00.1611).

a) are the user filtering operations still required as described in the tutorial, i.e. site filtering firstly SVAnnotator then GATK VariantFiltration?

b) is 'Alternate allele alignment' possibly only when breakpoint assembly is available, e.g. bam files after a TIGRA run?


Thanks


Wen