Changes between Version 24 and Version 25 of SOPs/variant_calling_GATK


Ignore:
Timestamp:
09/06/17 10:11:42 (7 years ago)
Author:
gbell
Comment:

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  • SOPs/variant_calling_GATK

    v24 v25  
    1515This example pipeline starts with a single-end short-read fastq file (Reads_1.fq).
    1616\\ \\
    17 Note that '''GATK requires Java 1.7''' (so you may need to adjust your path to point to that version, if an older version is the default).\\
     17Note that '''GATK (versions 3.7 and 3.8) requires Java 1.8''' (so you may need to adjust your path to point to that version, if an older version is the default).\\
    1818For example, this can be added to ~/.bashrc: \\
    19 export PATH=/usr/lib/jvm/java-7-openjdk-amd64/bin:$PATH
     19export PATH=/usr/local/jre1.8/bin:$PATH
    2020\\ \\
    2121