GlfTrio - Revision history

Mktrost at 16:45, 1 May 2012

2012-05-01T16:45:58Z

← Older revision		Revision as of 12:45, 1 May 2012
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	[[Category:Software]]		[[Category:Software]]
	=<~~span~~ style="color:#~~FF0000~~">~~glfTrio~~ has been ~~deprecated~~ and [[Polymutt]] ~~is the recommended replacement~~</~~span~~>=		{\| 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 [[Polymutt]]</div>
			\|}

	'''glfTrio''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes three [[GLF]] format genotype likelihood files as input and generates a [[VCF]]-format set of variant calls as output.		'''glfTrio''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes three [[GLF]] format genotype likelihood files as input and generates a [[VCF]]-format set of variant calls as output.

2012-04-17T13:46:44Z

← Older revision		Revision as of 09:46, 17 April 2012
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	[[Category:Software]]		[[Category:Software]]
	=glfTrio has been deprecated and [[Polymutt]] is the recommended replacement=		=<span style="color:#FF0000">glfTrio has been deprecated and [[Polymutt]] is the recommended replacement</span>=

2012-04-17T13:45:31Z

← Older revision		Revision as of 09:45, 17 April 2012
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	[[Category:Software]]		[[Category:Software]]
			=glfTrio has been deprecated and [[Polymutt]] is the recommended replacement=


	'''glfTrio''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes three [[GLF]] format genotype likelihood files as input and generates a [[VCF]]-format set of variant calls as output.		'''glfTrio''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes three [[GLF]] format genotype likelihood files as input and generates a [[VCF]]-format set of variant calls as output.

2010-08-14T05:27:00Z

X Chromosome Variant Calling

← Older revision		Revision as of 01:27, 14 August 2010
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	--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)		--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)

	For NCBI genome build 36, you should use the settings --xChr X --xStart 2709521 --xStop 154584237		For NCBI genome build 36, you should use the settings <code>--xChr X --xStart 2709521 --xStop 154584237</code>

	For NCBI genome build 37, you should use the settings --xChr X --xStart 2699520 --xStop 154931044		For NCBI genome build 37, you should use the settings <code>--xChr X --xStart 2699520 --xStop 154931044</code>

	== Model for Variant Calling ==		== Model for Variant Calling ==

2010-08-14T05:26:32Z

X Chromosome Variant Calling

← Older revision		Revision as of 01:26, 14 August 2010
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	--xStart ''sexChromosomeStart'' Start of the non-pseudo-autosomal portion of the X (2,709,521 bp in build 36)		--xStart ''sexChromosomeStart'' Start of the non-pseudo-autosomal portion of the X (2,709,521 bp in build 36)
	--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)		--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)

			For NCBI genome build 36, you should use the settings --xChr X --xStart 2709521 --xStop 154584237

			For NCBI genome build 37, you should use the settings --xChr X --xStart 2699520 --xStop 154931044

	== Model for Variant Calling ==		== Model for Variant Calling ==

2010-05-07T23:15:16Z

← Older revision		Revision as of 19:15, 7 May 2010
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			[[Category:Software]]
	'''glfTrio''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes three [[GLF]] format genotype likelihood files as input and generates a [[VCF]]-format set of variant calls as output.		'''glfTrio''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes three [[GLF]] format genotype likelihood files as input and generates a [[VCF]]-format set of variant calls as output.

2009-11-15T05:32:51Z

TODO

← Older revision		Revision as of 01:32, 15 November 2009
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	== TODO ==		== TODO ==

			Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.

	When calling genotypes on the X chromosome, glfTrio should properly account for male offspring. Currently, it assumes the offspring are female ... because the offspring for the two deeply sequenced 1000 Genomes trios are both female.		When calling genotypes on the X chromosome, glfTrio should properly account for male offspring. Currently, it assumes the offspring are female ... because the offspring for the two deeply sequenced 1000 Genomes trios are both female.

2009-11-15T04:51:51Z

Filtering According to Depth and Map Quality

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	before a call is made. Without the --strict option, reads for individuals below the threshold are ignored.		before a call is made. Without the --strict option, reads for individuals below the threshold are ignored.

	--~~minDepth~~ ''threshold'' Positions where the read depth falls below this threshold will be excluded.		--minTotalDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.
	--~~maxDepth~~ ''threshold'' Positions where the read depth exceeds this threshold will be excluded.		--maxTotalDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.

	=== Sample Labels ===		=== Sample Labels ===

2009-11-15T04:51:22Z

Basic Usage Example

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	glfTrio -f NA19239.chrom20.SLX.glf -m NA19238.chrom20.SLX.glf -c NA19240.chrom20.SLX.glf \		glfTrio -f NA19239.chrom20.SLX.glf -m NA19238.chrom20.SLX.glf -c NA19240.chrom20.SLX.glf \
	--father NA19239 --mother NA19238 --child NA19240 \		--father NA19239 --mother NA19238 --child NA19240 \
	--minMapQuality 30 \		--minMapQuality 30 --minTotalDepth 0 --maxTotalDepth 1000 \
	-b YRI.chrom20.SLX.vcf > YRI.chrom20.SLX.log		-b YRI.chrom20.SLX.vcf > YRI.chrom20.SLX.log

2009-11-15T04:48:03Z

Basic Usage Example

← Older revision		Revision as of 00:48, 15 November 2009
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	Here is an example of how <code>glfTrio</code> works:		Here is an example of how <code>glfTrio</code> works:

	~~glfSingle~~ -g NA19240.chrom20.SLX.glf -b ~~NA19240~~.chrom20.SLX.vcf > ~~NA19240~~.chrom20.SLX.log		glfTrio -f NA19239.chrom20.SLX.glf -m NA19238.chrom20.SLX.glf -c NA19240.chrom20.SLX.glf \
			--father NA19239 --mother NA19238 --child NA19240 \
			--minMapQuality 30 \
			-b YRI.chrom20.SLX.vcf > YRI.chrom20.SLX.log

	== Command Line Options ==		== Command Line Options ==