genome/genome — pull request #111 by malachig (2014-10-15 22:58:41+00:00)
Title: clin-seq: snv-indel-report - account for multiple data types (e.g. exome and WGS) being combined

I recently observed that when we have cases (such as GST1) where we are producing both Exome and WGS data, the filtered snv-indel-report for coding variants looks correct but the filtered report for all non-coding+coding variants is unexpectedly small.

It appears that the default minimum coverage filter is removing variants that are well covered in the WGS but not well covered in Exome. In this report we want to (by default) require a minimum level of coverage across all *samples* (e.g. normal and tumor) but we do not need the minimum to be achieved for all data types of all samples. A variant is acceptable if it has minimum coverage in (Sample1: WGS OR Exome) AND (Sample2: WGS OR Exome).

This PR fixes this. I have also fixed the subject legends file so that it actually contains a useful summary of the counts being aggregated.