picard HSmetrics

[cmccabe]

New to picard and trying to run HSmetrics on Ubuntu 12.0.4 using a BAM file. I am trying to get the predicted off-target reads. Thanks.

[GenoMax]

How to use the command: http://picard.sourceforge.net/comman...ulateHsMetrics

Or is there an error that you have run into?

Provide specifics for relevant help.

[cmccabe]

picard HSmetrics

So to run the command:

CalculateHsMetrics TARGET_INTERVALS=epilepsy.bam

trying to calculate the predicted off-target reads on the Bed file I converted to a BAM using Bedtools. Is this BAM aligned if not how do I align it. I have the hg19 fasta or is there a better way? Thanks.

[Heisman]

One thing you need is a bed file of the target regions. Do you have this?

[cmccabe]

picard HSmetrics

Yes I do have a bed file of the targets and a bam file. I used the bedToBam tool in bedtools, but do not think it is aligned. Thanks.

[Heisman]

The .bam file is aligned, I think by definition. You can run the program with something like this:

java -jar Tools/picard-tools-1.92/CalculateHsMetrics.jar BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/pathTohg19/hg19.fa

[cmccabe]

picard

Do the three files need to be in a folder and where do I put this folder? Do I cd into a directory? The picard-tools is in /usr/bin, but in order to see it I have to run ls /usr/bin. Also, is there a command to find out the version of picard-tools that is installed? Thanks

java -jar Tools/picard-tools-1.92/CalculateHsMetrics.jar BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/pathTohg19/hg19.fa

[Heisman]

You need to specify the correct path to all of the files. It does not matter if they are in the same directory. If you type /usr/bin/picard-tools and hit the tab button, it will fill out the version directory for you most likely.

[cmccabe]

picard HSmetrics

  dnascopev@ubuntu:~/picardtools-1.72$ java -jar Tools/picard-tools-1.72/CalculateHsMetrics.jar BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt

Unable to access jarfile Tools/picard-tools-1.72/CalculateHsMetrics.jar. Thanks.

[GenoMax]

Don't use the code example posted by Heisman as is. It probably refers to a path that exists on Heisman's system. Do you actually have that directory on your machine?

I thought you had installed picard-tools from Ubuntu repository using "apt-get" yesterday.

[cmccabe]

picard HSmetrics

Yes I installed picard from apt-get. Thanks.

[GenoMax]

Picard tools from Ubuntu is an older version (i.e. v. 1.48 I think).

Give this command a try:

$ picard-tools CalculateHsMetrics BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt

If you get a file not found error then alternate version would be (assuming all these files are in the directory where you are running this command from)

$ picard-tools CalculateHsMetrics BI=./target_regions.bed TI=./target_regions.bed I=./epilepsy.bam O=./epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt

[Heisman]

Yes, sorry, make sure you use paths relevant to you.

[cmccabe]

picard HSmetrics

 picard-tools CalculateHsMetrics BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt

 picard-tools CalculateHsMetrics BI=./target_regions.bed TI=./target_regions.bed I=./epilepsy.bam O=./epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt

ERROR: Unrecognized option: R

all three files are in the same directory (picardtools-1.72) Thank you.

[Heisman]

Type "picard-tools CalculateHsMetrics", hit enter, and copy/paste the output here.