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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