Changes

CalcMatch is a C/C++ software developed by Yun Li that 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 =

== --impped --impdat specify one input pedigree set. <br> ==

== --impped --impdat <br> ==

specify one input pedigree set.  

== --trueped --truedat specify the other input pedigree set. ==

== --trueped --truedat <br> ==

specify the other input pedigree set.

== --match ==  

== --match ==  

generates a matrix taking values 0,1,2 indicating # of matched alleles. The dimension of the matrix is # of overlapping individuals times # of overlapping markers of the two input pedigree sets.  

generates a matrix taking values 0,1,2 indicating # of matched alleles. The dimension of the matrix is # of overlapping individuals times # of overlapping markers of the two input pedigree sets.  

--bySNP is turned on by default to generate SNP specific measures. The output .bySNP will contain the following 6 fields for each SNP:  

== --bySNP ==

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&nbsp;: SNP name

     (1) SNP&nbsp;: SNP name

     (6) maskedG: total number of genotypes evaluated/masked (&lt;=n of course) (I should change the naming to comparedG or evaluatedG)

     (6) maskedG: total number of genotypes evaluated/masked (&lt;=n of course) (I should change the naming to comparedG or evaluatedG)

<br> --byGeno can be added on top of --bySNP. It will generates the following fields after the 6 fields above:  

<br>  

 

== --byGeno ==

can be added on top of --bySNP. It will generates the following fields after the 6 fields above:  

     (7) hetAerr : allelic discordance rate among heterozygotes

     (7) hetAerr : allelic discordance rate among heterozygotes

<br>

<br>

--accuracyByGeno is an option I added most recently to represent the above (7-20) information in a different way. Similar to --byGeno, it is used on top of --bySNP. It can be used together with --byGeno. It will generate the following fields, after (7-20) is --byGeno is turned on or after the 6th field otherwise.  

== --accuracyByGeno ==

Similar to --byGeno, it is used on top of --bySNP. It may be used together with --byGeno. It will generate the following fields, after (7-20) is --byGeno is turned on or after the 6th field otherwise.  

     (A) almajor: major allele

     (A) almajor: major allele

     (F) accuracy22: allelic concordance rate for homozygotes minor allele

     (F) accuracy22: allelic concordance rate for homozygotes minor allele

<br> --byPerson generates a separate output file .byPerson and contains the following information for each person:  

<br>  

== --byPerson ==

generates a separate output file .byPerson and contains the following information for each person:  

     (1) famid

     (1) famid

     (7) maskedG

     (7) maskedG

<br> This --bySNP option is useful if there is potential sample swap or inter-individual difference, e.g., sequencing depth, number of markers genotyped.  

<br> This --byPerson option is useful if there is potential sample swap or inter-individual difference, e.g., sequencing depth, number of markers genotyped.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Will generate CalcMatch.Output.bySNP (6+20+6 fields only) and CalcMatch.Output.byPerson.

<br> 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.

Please go to http://csg.sph.umich.edu//yli/software.html