SNP annotation
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Adrián • 0
Last seen 27 days ago


I am trying to perform a GWAS performed with a custom Illumina array (MS Chip). I have an annotation data frame which contains IlluminaID (for example that column contains entries like this one: "exm-rs1003581-131_B_F_1990477648") another column which contain names (some are in this format "exm-rs1003582" and some are in this "exm-IND6-167673849"). Other columns contain chromosome, AddressID_A (integer), AddressID_B (which are mostly empty). On the other hand I have a gds file which contains SNPs in the format "exm2231095". I am trying to use GWAStools to analyze this data. GWAStools requires for the AnnotationDataset a snpID variable which must be an integer, but that does no correspond with the SNP ID in the gds file and then it doesn't recognize the SNP ID. Does anyone know how to deal with this problem?

Thank you

SNPRelate SNP GWASTools Annotation GWASdata • 68 views

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