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CalcMatch is a C/C++ software developed by [https://www.sph.umich.edu/csg/yli/ Yun Li]. It compares two sets of pedigree files. It was initially written to compare imputed genotypes with their true/experimental counterpart but can be used to compare the concordance between any two sets of pedigree files. The input data are in standard Merlin/QTDT format (http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html).
CalcMatch is a C/C++ software developed by [https://csg.sph.umich.edu//yli/ Yun Li]. It compares two sets of pedigree files. It was initially written to compare imputed genotypes with their true/experimental counterpart but can be used to compare the concordance between any two sets of pedigree files. The input data are in standard Merlin/QTDT format (http://csg.sph.umich.edu//abecasis/Merlin/tour/input_files.html).
= Options =
= Options =
== --bySNP ==
== --bySNP ==
is turned on by default to generate SNP specific measures. The output .bySNP will contain the following 6 fields for each SNP:
is turned on by default (which means: if you put --bySNP in command line, it will be turned OFF!) to generate SNP specific measures. The output .bySNP will contain the following 6 fields for each SNP:
(1) SNP : SNP name
(1) SNP : SNP name
== --byGeno ==
== --byGeno ==
NOTE: this option is turned on by default. If you put --byGeno in command line, it will be turned OFF!
can be added on top of --bySNP. It will generates the following fields after the 6 fields above:
can be added on top of --bySNP. It will generates the following fields after the 6 fields above:
== --maskflag --maskped --maskdat ==
== --maskflag --maskped --maskdat ==
CalcMatch compares all genotypes overlapping the two input sets. However, when --maskflag is turned on AND --maskped and --maskdat are specified (I know ...) it compares only the following subset of the overlapping genotypes: genotypes either not found (i.e., individual or marker not included) or missing (included but with value 0/0, N/N, ./. etc) in --maskped / --maskdat. These options are useful when some individuals were masked for some SNPs while others masked for a different set of SNPs.
CalcMatch compares all genotypes overlapping the two input sets. However, when --maskflag is turned on AND --maskped and --maskdat are specified (I know ...) it compares only the following subset of the overlapping genotypes: genotypes either not found (i.e., individual or marker not included) or missing (included but with value 0/0, N/N, ./. etc) in --maskped / --maskdat. These options are useful when some individuals were masked for some SNPs while others masked for a different set of SNPs.
= output files =
== .bySNP ==
See option --bySNP <br>
== .byPerson ==
See option --byPerson <br>
== .minusstrand ==
Reports the list of SNPs that appear in minus strand (that is, SNPs for which more than two alleles are seen when combining imputed and true pedigree files. This file will only be generated if --byGeno or --accuracyByGeno is turned on. The former option --byGeno is turned on by default. <br>
= example command lines =
= example command lines =
Will generate CalcMatch.Output.bySNP (6+20+6 fields only) and CalcMatch.Output.byPerson.
Will generate CalcMatch.Output.bySNP (6+20+6 fields only) and CalcMatch.Output.byPerson.
= Download =
Please go to http://csg.sph.umich.edu//yli/software.html
