Review for "sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors"

Completed on 23 Aug 2016

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Comments to author

Author response is in blue.

The writing in the manuscript is much improved. The authors have responded to my other concerns. The manuscript should now be accepted, subject to the following minor corrections:

p5, line 116: expect should be except.

p8, line 211: welch should be Welch.

The changes have been made as recommended.

p12, line 335: Deconvolute is not the best word here, perhaps resolve. I leave this to the authors.

We replaced 'deconvolute' with resolve.

The computational requirements of the method are important practical details. It is essential to provide more details of the compute resources required (p10, line 256). How long does pre-processing take? The timings for the estimation step are for 12 CPUs. Presumably actually refers to cores rather than CPUs, with the problem split up across multiple cores (or perhaps not). Please clarify this. What state the chip type used?

We meant 12 cores, not 12 CPUs. The preprocessing step takes approximately 5 hours utilising 22 cores (1 per autosome).