sortsam. picard

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2.7 years ago

munche17live • 0

i have a few problems installing picard on my PC. any help available with the various commands i can use?

picard • 1.3k views

ADD COMMENT • link updated 2.7 years ago by Ram 43k • written 2.7 years ago by munche17live • 0

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How did you try to "install" picard? What errors are you facing? Give us as much information as you can.

ADD REPLY • link 2.7 years ago by Ram 43k

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Unable to access jarfile

ADD REPLY • link 2.7 years ago by munche17live • 0

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Is that "as much information as you can give us"? You've not told us what you've tried. Can you write a step-by-step process that can be followed by anyone to reproduce your issue?

ADD REPLY • link 2.7 years ago by Ram 43k

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I am done with my alignment of the .fasta file to my reference sequence.

I have a .sam file I want to convert to a.bam file.

after which I will use the same package for marking doubles.

https://broadinstitute.github.io/picard/

after downloading from the above site and following the command : java -jar $PICARD -h to test installation

I receive: Unable to access jarfile

ADD REPLY • link updated 2.7 years ago by Ram 43k • written 2.7 years ago by munche17live • 0

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Did you follow the 'environment variable' link and use the steps listed there to set the environment variable $PICARD to the right value? $PICARD should contain to the path to the Picard jar file. What is the output to echo $PICARD?

ADD REPLY • link 2.7 years ago by Ram 43k

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Here: https://broadinstitute.github.io/picard/

ADD REPLY • link updated 2.7 years ago by Istvan Albert 100k • written 2.7 years ago by brunobsouzaa ▴ 830

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thank you . i am assuming i have issues with the environment variable needed for picard

ADD REPLY • link 2.7 years ago by munche17live • 0

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