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Revision as of 07:49, 19 September 2011
, 07:49, 19 September 2011→Reference Haplotype Set
: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]].
: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]].
: Each line in the reference haplotype file starts with a haplotype label. This is followed by a series of alleles (one character per marker), optionally separated by whitespace to improve readability. Acceptable allele labels are "A", "C", "G", "T"; upper and lower case letters are treated identically. The digits "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G", "T".
: Each line in the reference haplotype file starts with a haplotype label. This is followed by a series of alleles (one character per marker), optionally separated by whitespace to improve readability. Acceptable allele labels are "A", "C", "G", "T"; upper and lower case letters are treated identically. The digits "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G", "T".
; --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].
== Target Haplotype Set ==
== Target Haplotype Set ==
