Review for "Indexcov: fast coverage quality control for whole-genome sequencing"

Completed on 20 Jul 2017 by .

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Sourced from https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/gigascience/6/11/10.1093_gigascience_gix090/2/gix090_reviewer-1-report-(original-submission).pdf?Expires=1520008218&Signature=OCWS7MI0f0cCwWTKHA-XWv0n5LqI0me2mgtMcmlRCnn7TgJNsyJYz38IdxNODLvBFZGjtwhtcvJK1KFM0hlTIZVRSYbCp-X66-357O1sO2Ze7vuKIdtq9gciGmk6NQY3DGBmfTOZMlXhl8aM9mxGVsNw-0mnA~-KIRFi8TWwq6fsdKwObTEXPCbPuveXCiaqXogNH7aE3o6P9-7BRkGL3Blu7LxukugskIfytP1nMUpFQGgLz~AKlIxXn2kZ8QNNeefCjNS3l02hxV7~tOsIwGFz1GJfhNc4HVyV8JlOC5ZIiAQtM-yTpeB5CcwpvJgU8Qbd0JSmsC94lZBHCFXoRQ__&Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q In their paper , the authors use the BAM index (bai) to get a rough idea of the presence of CNV . The idea is really original and the implementation is open-source. I don't have much to say about the paper itself: it's clear, with convincing examples. But, the main point is that I've used this software on a set of more than 500 WGS data: the processing was quick and within a few minutes we have (probably) detected a large somatic deletion in one of our sample that was unknown to us.On my side, the paper can be accepted without revision as is. If you have the opportunity to update the paper, I'd like to hear that the estimation of the number of reads is not only biased by the number of supplementary reads but also by the duplicate/MAQ=0/failing

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QC etc... Furthermore it's not clear to me if how this software would work if the majority of the reads were long reads (>17kb) ?

Pierre Lindenbaum