Changes between Version 7 and Version 8 of SOPs/variant_calling_GATK


Ignore:
Timestamp:
02/05/14 13:34:34 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/variant_calling_GATK

    v7 v8  
    1010export PATH=/usr/lib/jvm/java-7-openjdk-amd64/bin:$PATH
    1111\\ \\
     12Also note that GATK is not designed to use RNA-Seq data, in particular reads that are mapped across splice junctions.  If one still wants to use GATK for experiments of this type, one needs to do one of the following:
     13  * remove reads that map across splice junctions (e.g., those containing 'N' in the CIGAR string
     14  * map with a non-splice mapper (like bwa or bowtie, rather than tophat)
     15  * run GATK with the '--filter_reads_with_N_cigar' option
     16
    12171 - '''Index the reference genome.''' [Need to do just once, with [[http://samtools.sourceforge.net/samtools.shtml|samtools]].]
    1318  * samtools faidx /path/to/genome/genome.fa