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.

This will be updated more to make the progress easier.