Hi, I am using the imputed dosage files for [syn3157329](syn3157329) In the first column of the dosage file, some are in rsID, while others are in chrID: position. For those in chrID:position, which genome references were they built? Thank you in advance. Hui-Wen Yang syn3157329

Created by Hui-Wen Yang hyang39
Dear Abby, That was clear now. We also checked some of the chrIDs, confirming that some of the ChrID can only be found in GRCh37 (not found in GRCh36 or GRCh38) and the type of variant alleles consistent. We also checked some of the allele frequencies between the dosage and gnomAD browser, confirming that they are comparable. Thanks again for your efficient reply and great help. Hui-Wen
Hi Hui-Wen, sorry for the confusion. You are right, the 1000 Genome project announcement page mentions both assemblies, but since the method description for the dosage files says that they used the "1000 Genomes Project Consortium interim phase I haplotypes, 2010-2011 data freeze", I believe that means they used the GRCh37, since GRCh38 was not released until 2013.
Dear Abby, I am sorry for the back and forth. As GRCH37=hg19(not hg18) while GRCH36 = hg18, and the link of 1000 Genome project mentioned both assemblies, I am still not sure which genome build was used in the dosage file. Thank you again. Hui-Wen Yang
Hi Abby. Yes, I was asking about the genome build (sorry for the confusion). Now I see, they are GRCh37/hg18. Thank you so much for your reply.! Hui-Wen Yang
Hi Hui-Wen, my apologies, you were asking about the genome build. For 1000 Genomes the build is GRCh37/hg18 (https://www.internationalgenome.org/announcements/)
Hi Hui-Wen, in the assay description for the SNP array data here https://www.synapse.org/#!Synapse:syn3157325, it says that the imputed genotypes used 1000 Genomes as a reference (make sure you click "Show more" in the wiki and scroll down to the end of the last paragraph). Does that answer your question?

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