handy tool for exome sequencing quality control

[mrfox]

Hi all,

What tool are you using for the quality control of whole-exome sequencing data after mapping the reads to the genome? I would like to have a handy tool to count the total reads and the total uniquely mapped reads, calculate the coverage on the exome to estimate the data quality.

Any recommendation will be appreciated.

Thank you.

[caddymob]

Check out CalculateHsMetrics from Picard:
http://picard.sourceforge.net/comman...ulateHsMetrics