paired read with unregular insert size.

[hujiacun]

Hi,
Is there any method to pick out paired reads with a bad insert size , just as those above 1kb. If I can sort them out and caculate their coverage at one locus, I can detect a Structure variation.
Thanks!

[diego diaz]

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

https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php