[BioC] cn.mops: copy number for low-coverage bam files?

[Paul Shannon]

I'd like to take advantange of the segmentation algorightms in cn.mops, to estimate copy number from low-coverage BAM files.  The average coverage in our tumor and normal DNA, is about 0.8 and 0.7 respectively, quite uniformly across the whole genome.   The consistency of the reads, and their ratios, allow us to plausibly identify amplifications and deletions, either visually, or by simple calculations.  Now it's time for more rigor, for which I turned to cn.mops.

However, it appears that such low-coverage sequencing is apparently not well-suited to cn.mops.

The man page says:

  minReadCount: If all samples are below this value the algorithm will, return the prior knowledge. 
  This prevents that the algorithm, from being applied to segments with very low coverage.   Default=1.

Even if I set minReadCount to 0.2, no useful results are returned:

Individual CNVs: 
GRanges with 2 ranges and 4 metadata columns:
     seqnames                 ranges strand |           sampleName    median      mean        CN
        <Rle>              <IRanges>  <Rle> |             <factor> <numeric> <numeric> <logical>
 [1]    chr10 [ 42441001,  42553000]      * | F7272LUNG.sorted.bam 0.5849625 0.5767351      <NA>
 [2]    chr10 [135478001, 135534746]      * | F7272SCLC.sorted.bam 0.2196978 0.5403949      <NA>

Before I give up on using this impressive package, may I ask if there is indeed a way to use it with low-coverage but otherwise high-quality bam files?

Thanks!

- Paul