I have 2 questions about the Picard metrics.
Sorry if they are stupid or you have already answered but I didn't find anything googling or searching in this forum.
1. HsMetrics: in the page of metrics definition it is declared that the tool returns the percentage of all target bases achieving 2x,10x,20x,30,40x,50x,100x but when I run the command in the output file there are only 2x,10x,20x,30x.
Is that correct? Is there any option I have to use to add information about 40x,50x and 100x?
My command is:
java -jar CalculateHsMetrics.jar \
- In the PICARD metric page I found metrics about VariantCalling:
But I didn't find the associated Picard tool. Is that an old metric not in use anymore?
Thanks for the help, hope to not bother you.
java -jar CalculateHsMetrics.jar --version
Linux version 2.6.32-279.2.1.el6.x86_64 ([email protected])