to get all the reads mapped in proper pair :
samtools view -F 3 yourbam.bam > properlypaired.bam
to get all the reads mapped in not proper pair :
samtools view -f 3 yourbam.bam > notproperlypaired.bam
Then to get the reads mapped to specific loci :
samtools view yourfile.bam chr1:2500-5000
then you can measure the coverage with GATK DepthOfCoverage
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This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.
The Headliner
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