File format conversion

[Aimen Zaidi]

I am working with genotype data from the 19K Brassica SNP array. My input file has the following header format:

SNPID Chrom Position Call Freq AB Freq 24CRA1-1 24CRA1-10 24CRA1-11 24CRA1-12 ...

However, I need to convert this data to HapMap format, which requires the following header:

rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode <genotype columns>

My question is: how should I handle the required HapMap columns like strand, assembly#, center, protLSID, assayLSID, panelLSID, and QCcode when I don’t have that metadata available in my dataset?

[Terry Casstevens]

You should be able to put NA for those fields

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