Changes

Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).  

Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).  

The latest reference panel generated by the 1000 Genomes project uses NCBI Build 37 (HG 19). Make sure that your data is on Build 37, otherwise lift your data over.

The latest reference panel generated by the 1000 Genomes project uses NCBI Build 37 (HG 19). Make sure that your data is on Build 37 (or Minimac may ignore genotyped markers whose names have changed in build 37). If you are trying to convert your data from an earlier genome build to build 37, you'll probably find the [ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz dbSNP merge table] ([http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch table description on the NCBI website]), which logs rs# changes between dbSNP builds, and the UCSC online [http://genome.ucsc.edu/cgi-bin/hgLiftOver liftOver tool], which converts genome positions between different genome builds, to be quite useful.

=== Quality Control ===

=== Quality Control ===