Picard tools - CalculateHsMetrics

[lre1234]

Hi all,
I am trying to use the CalculateHsMetrics of picard tools to calculate my exome coverage the command that I am using is this:

java -jar picard-tools-1.86/picard-tools-1.86/CalculateHsMetrics.jar BAIT_INTERVALS=regions.bed TARGET_INTERVALS=regions.bed INPUT=Final.bam OUTPUT=PicardCoverage.txt PER_TARGET_COVERAGE=Picard_PER_TARGET_COVERAGE.txt

When I add the PER_TARGET_COVERAGE flag, the program doesn't run and just gives me the help. If I remove this flag then the program runs just fine.

Any thoughts on what I might be doing wrong?

Thanks

[IsmailM]

Try to add VALIDATION_STRINGENCY to your command.

java -jar picard-tools-1.86/picard-tools-1.86/CalculateHsMetrics.jar BAIT_INTERVALS=regions.bed TARGET_INTERVALS=regions.bed INPUT=Final.bam OUTPUT=PicardCoverage.txt PER_TARGET_COVERAGE=Picard_PER_TARGET_COVERAGE.txt VALIDATION_STRINGENCY=LENIENT

[lre1234]

I just tried adding the VALIDATION_STRINGENCY=LENIENT, and it still doesn't work. It does run with out that!
Thanks for your help

[aggp11]

I know this might be silly, but just try changing the name of your PER_TARGET_COVERAGE file to not have "PER_TARGET_COVERAGE". may be just make it all lowercase.

I would be surprised if this worked.

[lre1234]

Nope! It was worth a try...

[aggp11]

Ok. So I ran your command on our system and I got the help menu with the following message:

Must supply REFERENCE_SEQUENCE when supplying PER_TARGET_COVERAGE

and so you need to provide your REFERENCE_SEQUENCE and this should work.

[lre1234]

That seems to work!!! It's running now. I never got an error that said that the reference was needed!
Thanks alot!!!