Changes between Version 4 and Version 5 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
08/15/17 09:53:01 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v4 v5  
    66
    77== Using GATK to call variants from RNA-seq reads ==
     8This example pipeline starts with a single-end short-read fastq file (Reads_1.fq).
     9\\ \\
     10Note 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).\\
     11For example, this can be added to ~/.bashrc: \\
     12export PATH=/usr/lib/jvm/java-7-openjdk-amd64/bin:$PATH
     13\\ \\