BamGenotypeCheck - Revision history

Ppwhite: /* Download bamGenotypeCheck */

2017-02-02T15:11:17Z

Download bamGenotypeCheck

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

	To get a copy go to the [http://~~www~~.sph.umich.edu/~~csg~~/pha/karma/download/ Karma Download] download page.		To get a copy go to the [http://csg.sph.umich.edu//pha/karma/download/ Karma Download] download page.


	== Build bamGenotypeCheck ==		== Build bamGenotypeCheck ==

Mktrost: Update Deprecated info

2012-05-01T16:03:39Z

Update Deprecated info

← Older revision		Revision as of 12:03, 1 May 2012
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	~~'''THIS PAGE/TOOL IS~~ DEPRECATED ~~- see~~ [[VerifyBamID]]~~'''~~		{\| style="width:100%; background:#FF8989; margin-top:1.2em; border:1px solid #ccc;" \|
			\| style="width:100%; text-align:center; white-space:nowrap; color:#000;" \|
			<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">This tool has been DEPRECATED, and replaced by [[VerifyBamID]]</div>
			\|}

	'''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).		'''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).

Mktrost at 19:06, 27 March 2012

2012-03-27T19:06:11Z

← Older revision		Revision as of 15:06, 27 March 2012
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			'''THIS PAGE/TOOL IS DEPRECATED - see [[VerifyBamID]]'''

	'''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).		'''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).

Pha: fix indenting

2010-07-16T17:06:33Z

fix indenting

← Older revision		Revision as of 13:06, 16 July 2010
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	= Download bamGenotypeCheck =		== Download bamGenotypeCheck ==

	To get a copy go to the [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download] download page.		To get a copy go to the [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download] download page.


	= Build bamGenotypeCheck =		== Build bamGenotypeCheck ==

	Karma (which includes bamGenotypeCheck) is designed to be reasonably portable.		Karma (which includes bamGenotypeCheck) is designed to be reasonably portable.

Pha: add pointer to fresh karma download

2010-07-16T17:05:10Z

add pointer to fresh karma download

← Older revision		Revision as of 13:05, 16 July 2010
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	'''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).		'''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).


			= Download bamGenotypeCheck =

			To get a copy go to the [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download] download page.


			= Build bamGenotypeCheck =

			Karma (which includes bamGenotypeCheck) is designed to be reasonably portable.

			However, since development occurs only on Ubuntu 9.10 x86 and x64 platforms, and later, there are likely other portability issues.

			We support Karma only on Ubuntu 9.10 and later on 64-bit processors.

	== Usage ==		== Usage ==

Pha: /* Input Files */ fix link

2010-06-22T14:57:18Z

Input Files: fix link

← Older revision		Revision as of 10:57, 22 June 2010
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	=== Input Files ===		=== Input Files ===

	-r ''genome reference in [[http://en.wikipedia.org/wiki/Fasta_format\|simplified FASTA format]]''		-r ''genome reference in [http://en.wikipedia.org/wiki/Fasta_format simplified FASTA format]''
	-a ''allele Frequency file in [[MERLIN format]]''		-a ''allele Frequency file in [[MERLIN format]]''
	-p ''pedigree file in [[MERLIN format]]''		-p ''pedigree file in [[MERLIN format]]''

Pha: /* Input Files */ add fasta link

2010-06-22T14:56:05Z

Input Files: add fasta link

← Older revision		Revision as of 10:56, 22 June 2010
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	=== Input Files ===		=== Input Files ===

	-r ''FASTA format ~~genome reference~~''		-r ''genome reference in [[http://en.wikipedia.org/wiki/Fasta_format\|simplified FASTA format]]''
	-a ''allele Frequency file in [[MERLIN format]]''		-a ''allele Frequency file in [[MERLIN format]]''
	-p ''pedigree file in [[MERLIN format]]''		-p ''pedigree file in [[MERLIN format]]''

Pha: /* Input Files */ more detail

2010-06-22T14:54:21Z

Input Files: more detail

← Older revision		Revision as of 10:54, 22 June 2010
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	-r ''FASTA format genome reference''		-r ''FASTA format genome reference''
	-a ''allele Frequency file''		-a ''allele Frequency file in [[MERLIN format]]''
	-p ''pedigree file in [[MERLIN format]]''		-p ''pedigree file in [[MERLIN format]]''
	-d ''data file in [[MERLIN format]]''		-d ''data file in [[MERLIN format]]''

Pha: /* Filtering */ add -f option

2010-06-22T14:53:20Z

Filtering: add -f option

← Older revision		Revision as of 10:53, 22 June 2010
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	=== Filtering ===		=== Filtering ===

	-b [int] ''exclude bases with quality less than [int]''		-b [int] ''exclude bases with quality less than [int]''
	-M [int] ''exclude reads with map quality less than [int]''		-M [int] ''exclude reads with map quality less than [int]''
	-F [int] ''set custom BAM flags filter (not implemented at the moment)''		-f [float] ''drop markers with minor allele frequency smaller than [float]''
			-F [int] ''set custom BAM flags filter (not implemented at the moment)''

	=== Other Options ===		=== Other Options ===

Pha: rename again

2010-06-22T14:47:38Z

rename again

← Older revision		Revision as of 10:47, 22 June 2010
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	'''~~genotypeIdCheck~~''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).		'''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).

	== Usage ==		== Usage ==
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	A key step in any genetic analysis is to verify whether data being generated matches expectations. This program checks whether reads in a BAM file match previous genotypes for a specific sample.		A key step in any genetic analysis is to verify whether data being generated matches expectations. This program checks whether reads in a BAM file match previous genotypes for a specific sample.

	Using a mathematical model that relates observed sequence reads to an hypothetical true genotype, ~~genotypeIdCheck~~ tries to decide whether sequence reads match a particular individual or are more likely to be contaminated (including a small proportion of foreign DNA), derived from a closely related individual, or derived from a completely different individual.		Using a mathematical model that relates observed sequence reads to an hypothetical true genotype, bamGenotypeCheck tries to decide whether sequence reads match a particular individual or are more likely to be contaminated (including a small proportion of foreign DNA), derived from a closely related individual, or derived from a completely different individual.

	== Basic Usage Example ==		== Basic Usage Example ==
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	Here is a typical command line:		Here is a typical command line:

	~~genotypeIDcheck~~ -r /data/local/ref/karma.ref/human.g1k.v37.fa \		bamGenotypeCheck -r /data/local/ref/karma.ref/human.g1k.v37.fa \
	-k BAMfiles.txt -p test.ped -d test.dat -m test.map		-k BAMfiles.txt -p test.ped -d test.dat -m test.map

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	For each aligned base that overlaps a known genotype, we calculate the probability the probability that it was derived from a particular known genotype. This comparison considers only bases that overlap previously known genotypes and that meet the base quality and mapping quality thresholds.		For each aligned base that overlaps a known genotype, we calculate the probability the probability that it was derived from a particular known genotype. This comparison considers only bases that overlap previously known genotypes and that meet the base quality and mapping quality thresholds.

	Each individual in a pedigree has a different combination of genotypes, and ~~genotypeIdCheck~~ will systematically search for the individual whose genotypes best match the observed read data.		Each individual in a pedigree has a different combination of genotypes, and bamGenotypeCheck will systematically search for the individual whose genotypes best match the observed read data.

	For more about the technical details, see the page [[Verifying Sample Identities - Implementation]]		For more about the technical details, see the page [[Verifying Sample Identities - Implementation]]

	== TODO ==		== TODO ==