<p>Physical (or fragment) coverage means counting also the unsequenced part of the fragment between properly mapped read pairs. As output I&#39;d like to get a frequency table that tells me how many bases are covered how many times. I could not find an easy solution for this problem using standard tools only (SAMtools, BEDtools, GATK).</p>

<p>EDIT: The reason why I am interested in physical coverage is because I think this is quite a useful metric when it comes to assess the power of a WGS data set to detect structural variations.</p>

<p>You can do this in three steps using bedtools. First convert your paired-end BAM file to a BEDPE formated file of fragments with bedtools bamToBed, then use cut to convert BEDPE to BED, then use bedtools genomecov to compute coverage from the resulting BED file of fragments. See this the section after NOTES in this post at the bedtools mailing list for more information: https://groups.google.com/forum/#!msg/bedtools-discuss/kulRA_7Ybow/4Be6otCybZgJ</p>
