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pindel.sh
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pindel.sh
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TUMOR_BAM=`echo $1 | sed "s:\.bam::g"`
export SAMTOOLS='/hematology/tools/samtools/samtools'
export PINDEL='/hematology/tools/pindel/pindel'
$SAMTOOLS view -b ${TUMOR_BAM}.bam chr13:28606093-28610689 1> ${TUMOR_BAM}_pindel.bam
$SAMTOOLS index ${TUMOR_BAM}_pindel.bam
#-----------------------------------------------------------------
# Run Pindel
#-----------------------------------------------------------------
echo "${TUMOR_BAM}_pindel.bam 600 ${TUMOR_BAM}" > ${TUMOR_BAM}_conf.txt
$PINDEL -i ${TUMOR_BAM}_conf.txt -f $REFERENCE -o ${TUMOR_BAM}_pindel -c 'chr13:28565921-28702250' -r false --report_interchromosomal_events false
rm ${TUMOR_BAM}_conf.txt
$PINDEL2VCF -p ${TUMOR_BAM}_pindel_TD -r $REFERENCE -R RefGene -d 20140901 -v ${TUMOR_BAM}_pindel_TD.vcf
$PINDEL2VCF -p ${TUMOR_BAM}_pindel_SI -r $REFERENCE -R RefGene -d 20140901 -v ${TUMOR_BAM}_pindel_SI.vcf
exit 0