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.
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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.
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picard HSmetrics
So to run the command:
Code:CalculateHsMetrics TARGET_INTERVALS=epilepsy.bam
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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
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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
Code: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
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picard HSmetrics
Code: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
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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.
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Picard tools from Ubuntu is an older version (i.e. v. 1.48 I think).
Give this command a try:
Code:$ picard-tools CalculateHsMetrics BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt
Code:$ picard-tools CalculateHsMetrics BI=./target_regions.bed TI=./target_regions.bed I=./epilepsy.bam O=./epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt
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picard HSmetrics
Code:picard-tools CalculateHsMetrics BI=target_regions.bed TI=target_regions.bed I=epilepsy.bam O=epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt
Code:picard-tools CalculateHsMetrics BI=./target_regions.bed TI=./target_regions.bed I=./epilepsy.bam O=./epilepsy.CalculateHSmetrics R=/picardtools-1.72/hg19_fasta.txt
all three files are in the same directory (picardtools-1.72) Thank you.
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