based on a WES project of cancer bam files for variant calling purposes, I'm currently trying to collect some specific quality metrics-namely the on target coverage for each bam file. Based on a small search, I found than Picard is capable of this analysis, through the following function
In detail, based on the protocol library kit used for the experimental design [SureSelect Clinical Research Exome V2, Agilent Technologies], i used the following link:
and selected the same kit for downloading the necessary bed files- SureSelect Clinical Research Exome V2 (Design ID-S30409818). My main issue is the following:
As the function arguments are the following:
java -jar picard.jar CollectHsMetrics \ I=input_reads.bam \ O=output_hs_metrics.txt \ R=reference.fasta \ BAIT_INTERVALS=bait.interval_list \ TARGET_INTERVALS=target.interval_list
However, the files downloaded from agilent, included the following "name prefix" files:
_AllTracks.bed, _Covered.bed, _Padded.bed, _Regions.bed and a file named Targets.txt
1) Which of the above files should i use with the arguments BAIT_INTERVALS and TARGET_INTERVALS, respectively ?
2) Or alternatively, i have downloaded the wrong files, and i should search them in other repositories ?
Thank you in advance and excuse me for any naive questions, but it is the first time that I'm trying to compute on target coverage !!