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SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

For a list of the official rules, visit (https://www.seqanswers.com/forum/sit...wledge-and-win)
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  • Reg Picard MarkDuplicates

    Hi

    I am beginner in python. I am trying to automate the process of variant calling for the whole genome sequencing data for plants in ubuntu. We wrote commands for each software (by giving path) and integrated all software's in python. I am having a problem when i execute the script, where the script file could not run picard tools Mark Duplicates. It did not give any error but process wont continue after that, whereas when i use same tool, picard markduplicates in terminal its working fine without any error. Can anyone help me in trouble shooting this.

    Example script that we wrote

    import subprocess,os,commands

    m=raw_input("Enter the project destination")

    os.environ["JAVA_HOME"]="/usr/java/jdk1.8.0_121/lib/visualvm/platform/modules"

    os.chdir('/home/sukesh/picard-tools')

    os.system('java -jar picard.jar MarkDuplicates I='+m+'/6SAMTOBAM/sortIRGSP.bam
    O='+m+'/7MARKDUPS/dups.bam REMOVE_DUPLICATES=false METRICS_FILE=metricN.log ASSUME_SORTED=True VALIDATION_STRINGENCY=LENIENT')

    os.chdir('/home/Downloads')

    Or is there any other tool which can mark duplicates other than samtools which will be more helpful?

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