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  • db_index_sub.sh 462 B
    source /local/gensoft2/adm/etc/profile.d/modules.sh # module location path
    
    module add picard-tools/1.94 samtools/1.2 # add your modules 
    
    # Create picard index if it doesn't exist
    if [ ! -f {fasta_dict} ];
    then
        echo "### Picard index creation "
        CreateSequenceDictionary R= {ref_fasta} O= {fasta_dict}
    fi
    
    # Create samtools index if it doesn't exist
    if [ ! -f {fasta_fai} ];
    then
        echo "### Samtools index creation "
        samtools faidx {ref_fasta}
    fi