Hi :)

I am in search of an easy method to list all sequencing gaps for MiSeq-NexteraXT-Workflow.

The result should be a list of all target-regions (exons+20bp-padding) which at some point fall below a CoverageDepth of 50x. So we can reanalyze those exons via Sangerseq.

For Illumina-Enrichment Workflow this was easily done via the "gaps.csv"-File by modifying the samplesheet with "MinimumCoverageDepth,50". Sadly "gaps.csv" are not given in the NexteraXT-method :(

I am the typical Windows-User and was happy until now with Excel, VariantStudio and IGV-Browser :D Is there a way to get such a gaps-list without Linux-Command-Line-Tools like BedTools or is there no way around?

Thx a lot!