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  • paired read with unregular insert size.

    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!

  • #2
    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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