CalcMatch - Revision history

Ppwhite: /* Download */

2017-02-02T16:03:38Z

Download

← Older revision		Revision as of 12:03, 2 February 2017
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	= Download =		= Download =
	Please go to http://~~www~~.sph.umich.edu/~~csg~~/yli/software.html		Please go to http://csg.sph.umich.edu//yli/software.html

Ppwhite at 15:31, 2 February 2017

2017-02-02T15:31:55Z

← Older revision		Revision as of 11:31, 2 February 2017
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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 =

Ylwtx at 11:01, 28 January 2011

2011-01-28T11:01:55Z

← Older revision		Revision as of 07:01, 28 January 2011
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	== --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
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	== --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:

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	== --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 =

Ylwtx at 22:04, 11 January 2011

2011-01-11T22:04:31Z

← Older revision		Revision as of 18:04, 11 January 2011
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	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://www.sph.umich.edu/csg/yli/software.html

Ylwtx at 13:34, 21 October 2010

2010-10-21T13:34:29Z

← Older revision		Revision as of 09:34, 21 October 2010
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	CalcMatch is a C/C++ software developed by 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://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).

	= Options =		= Options =

Ylwtx at 03:00, 23 June 2010

2010-06-23T03:00:37Z

← Older revision		Revision as of 23:00, 22 June 2010
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	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 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).

	= Options =		= Options =

Ylwtx: /* example command lines */

2010-06-23T02:59:39Z

example command lines

← Older revision		Revision as of 22:59, 22 June 2010
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	Will generate CalcMatch.Output.bySNP (6+6 fields only) and CalcMatch.Output.byPerson.		Will generate CalcMatch.Output.bySNP (6+6 fields only) and CalcMatch.Output.byPerson.


	CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --accuracyByGeno --byGeno --byPerson		CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --accuracyByGeno --byGeno --byPerson

	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.

Ylwtx: /* example command lines */

2010-06-23T02:59:24Z

example command lines

← Older revision		Revision as of 22:59, 22 June 2010
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	= example command lines =		= example command lines =

			CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --byPerson

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

			CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --byGeno --byPerson

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

			CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --accuracyByGeno --byPerson

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


			CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --accuracyByGeno --byGeno --byPerson

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

Ylwtx at 02:55, 23 June 2010

2010-06-23T02:55:40Z

← Older revision		Revision as of 22:55, 22 June 2010
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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
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	(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
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	<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
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	(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
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	(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.

	<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.		= example command lines =

Ylwtx at 02:52, 23 June 2010

2010-06-23T02:52:34Z

← Older revision		Revision as of 22:52, 22 June 2010
Line 1:		Line 1:
	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 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).

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

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

	--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.		== --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.

	--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: