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Old 06-24-2013, 01:43 PM   #1
prs321
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Default Picard versus SAMtools ? Which one is better?

I can't even get Picard to run. I despise java and the syntax makes my eyes bleed.

Is it better for me to stick to SAMtools? I can actually get SAM tools to run and it is very straight forward to use.
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Old 06-24-2013, 01:47 PM   #2
snetmcom
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What is your main goal with either of these tools?
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Old 06-24-2013, 01:51 PM   #3
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I'm not really sure, I was just told that they are using for sorting, indexing, and such in order to prepare me for analysis of 20 genomes compared to the reference genome.
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Old 06-24-2013, 01:59 PM   #4
vivek_
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WHile Picard and samtools have certain common modules, there are many features that are exclusive to each tool.

I'm surprised by the not being able to run Picard comment though. Java is like the most platform independent language and you should be able to run Picard easily without any installation issues.
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Old 06-24-2013, 02:05 PM   #5
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Interesting... I tried to call the help command in the terminal after i loaded picard using "module load picard" and it didn't work. I can tried entering picard but it didnt work.

Then I checked to see if picard was actually loaded and it was. I'm confused as to what I am doing wrong at this point.
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Old 06-24-2013, 03:16 PM   #6
jimmybee
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While I agree with you on your comments on Java in general, picard is a nessessity for some things so I'd suggest giving it another try. I use samtools for indexing and sorting but Picard for conversions and the removal of duplicates. Perhaps your java run time environment is giving you the problems?
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Old 06-24-2013, 03:31 PM   #7
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Its helpful to post the actual commands you used, that way others can see if you are making a rather simple mistake.
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Old 06-25-2013, 05:24 AM   #8
prs321
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Quote:
Originally Posted by chadn737 View Post
Its helpful to post the actual commands you used, that way others can see if you are making a rather simple mistake.
I put into the command line the following:

module load picard
module list


After loading picard, I double checked to make sure it was loaded into the terminal and it was.

I tried using ./picard, picard, picard -h... nothing worked.

I don't get what I'm doing wrong because when I load software such as bwa, fastqc, or anything else I can run the program or get the list of commands associated with the program by typing in ./nameofprogram
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Old 06-25-2013, 05:40 AM   #9
chadn737
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Use:
Code:
java -Xmx2g -jar xxxxxx.jar <arguments>
for example:

Code:
java -Xmx2g -jar /path/to/SortSam.jar INPUT=example.sam OUTPUT=example.output.sam SORT_ORDER=coordinate
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Old 06-25-2013, 05:41 AM   #10
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ahh ok thank you! Much appreciated, it worked.
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