Changes

; --snpAliases [filename]

; --snpAliases [filename]

: This option points to a file listing mappings between alternate marker names. Each row should include two columns. The first column lists a previous commonly used name for a marker (perhaps from an earlier version of dbSNP) and the second column lists the current preferred name for the marker. An example input file, which maps ids from the 1000 Genomes Project and earlier versions of dbSNP to dbSNP build 134, see [http://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz dbsnp134-merges.txt.gz].

: This option points to a file listing mappings between alternate marker names. Each row should include two columns. The first column lists a previous commonly used name for a marker (perhaps from an earlier version of dbSNP) and the second column lists the current preferred name for the marker. An example input file, which maps ids from the 1000 Genomes Project and earlier versions of dbSNP to dbSNP build 134, see [http://csg.sph.umich.edu/abecasis/downloads/dbsnp134-merges.txt.gz dbsnp134-merges.txt.gz].

== Target Haplotype Set ==

== Target Haplotype Set ==