kits.md

Installation of Exome-Kits

The pipeline follows best-practices defined by the Broad Institute of MIT and Harvard. You need to specify the correct exome capture kits that were used to sequence your samples and prepare corresponding interval_list and dict files for that purpose.

First Step

Prepare sequence dictionary for your reference genome.

picard CreateSequenceDictionary O=GRCh37.dict R=GRCh37.fa 

Second Step

Prepare the interval_list files required by GATK for the analysis.

picard BedToIntervalList I=S03723314_Covered.bed O=S03723314_Covered.interval_list SD=GRCh37.dict 
picard BedToIntervalList I=S03723314_Regions.bed O=S03723314_Regions.interval_list SD=GRCh37.dict 

Then specify these in a config file as a new kit and you should be fine. Otherwise, you can also use the parameters to specify the required kit files for your exome capture kit.