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= 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 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
(6) maskedG: total number of genotypes evaluated/masked (<=n of course) (I should change the naming to comparedG or evaluatedG)
(6) maskedG: total number of genotypes evaluated/masked (<=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.
<br>
== --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.
= example command lines =
