samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bam.bai 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
# Split the deduped BAM file for multi-threaded tin calculation
for i in `samtools view ${repRID}.sorted.deduped.bam | cut -f3 | sort | uniq`;
do
echo "echo \"LOG: splitting each chromosome into its own BAM file with Samtools\" >> ${repRID}.dedup.err; samtools view -b ${repRID}.sorted.deduped.bam \${i} > ${repRID}.sorted.deduped.\${i}.bam"