Illumina Generated Manifest has no RefStrand column

[tbrunetti]

I have no problems running this using BPM, however, when using an Illumina provided manifest (.csv) it is missing the RefStrand header. These are the headers that were provided, can you tell me which one maps to RefStrand (I want to say it is likely SourceStrand, but I would like confirmation before changing a header name; if is is SourceStrand, should I update all SourceStrand embedded headers to be RefStrand)?:

IlmnID, Name, IlmnStrand, SNP, AddressA_ID, AlleleA_ProbeSeq, AddressB_ID, AlleleB_ProbeSeq, GenomeBuild, Chr, MapInfo, Ploidy, Species, Source, SourceVersion, SourceStrand, SourceSeq, TopGenomicSeq, BeadSetID

[jjzieve]

Which CSV manifest are you using? It should have a RefStrand column if it was created relatively recently. It is not the same as the SourceStrand.

[danilovkiri]

@jjzieve

Hi, I have exactly the same problem. The manifest is old (dated 2014), though I have to use it now to process old genotyping data. Is there a way (algorithmically) to assign RefStrand values based on whatever sequences can be found in SourceSeq/TopGenomicSeq/etc?

[jjzieve]

@danilovkiri You could try using the SourceSeq and comparing to the ProbeSeq values if you want, but I wouldn't recommend it. The way its done internally validates against the reference genome in case the SourceSeq isn't accurate (this can occur on custom designs). I would email techsupport@illumina.com and ask to get the RefStrand mapped on your manifest.

[danilovkiri]

Thank you very much @jjzieve

[jjzieve]

@danilovkiri No problem! Let me know if that works out for you. If so, I'll close this issue.