In my lab, we are genotyping some rs## using the Affymetrix GeneTitan technology.

Some rs## designed for our plates are now part of the RsMergeArch file.

"refSNP(rs) cluster is based on unique genome position. On new genome assembly, previously different contig may align. So different rs clusters map to the same location. In this case, we merge the rs. This table tracks this merging."

If I want to map such snp on the genome, I now need to map the new rsID on the genome. But how should I handle the orien2Current flag ($8) ? does '0' mean that the strand are the same ? or is it '1' ?

$1      rsHigh            rs1051721
$2      rsLow             rs7714
$3      build_id          102
$4      orien                 0
$5      create               2002-01-04 16:38:00.0
$6      updated            2006-03-11 06:48:00.0
$7      rsCurrent          rs1748
$8      orien2Current  1

And do you think I should do whith my genotypes called by the Affymetrix platform: should I reverse/complement the genotypes if "orien2Current" column has changed ($8) ?