Difference between revisions of "GlfTrio"
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+ | <div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">This tool has been DEPRECATED, and replaced by [[Polymutt]]</div> | ||
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'''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. | ||
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Here is an example of how <code>glfTrio</code> works: | Here is an example of how <code>glfTrio</code> works: | ||
− | + | glfTrio -f NA19239.chrom20.SLX.glf -m NA19238.chrom20.SLX.glf -c NA19240.chrom20.SLX.glf \ | |
+ | --father NA19239 --mother NA19238 --child NA19240 \ | ||
+ | --minMapQuality 30 --minTotalDepth 0 --maxTotalDepth 1000 \ | ||
+ | -b YRI.chrom20.SLX.vcf > YRI.chrom20.SLX.log | ||
== Command Line Options == | == Command Line Options == | ||
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=== Basic Output Options === | === Basic Output Options === | ||
− | -b '' | + | -b ''baseCallFile'' Specifies the name of the output [[VCF]]-format base call file |
-p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold'' | -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold'' | ||
--reference Positions called as homozygous reference will be included in the output. | --reference Positions called as homozygous reference will be included in the output. | ||
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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. | ||
− | -- | + | --minTotalDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded. |
− | -- | + | --maxTotalDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded. |
=== Sample Labels === | === Sample Labels === | ||
− | --father '' | + | --father ''fatherLabel'' Specifies a label for the male parent, which will be included in the output VCF file |
− | --mother '' | + | --mother ''motherLabel'' Specifies a label for the female parent, which will be included in the output VCF file |
− | --child '' | + | --child ''childLabel'' Specifies a label for the child, which will be included in the output VCF file |
=== X Chromosome Variant Calling === | === X Chromosome Variant Calling === | ||
− | --xChr '' | + | --xChr ''chromosomeName'' Label for the 'X' chromosome in the GLF file |
− | --xStart '' | + | --xStart ''sexChromosomeStart'' Start of the non-pseudo-autosomal portion of the X (2,709,521 bp in build 36) |
− | --xStop '' | + | --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 <code>--xChr X --xStart 2709521 --xStop 154584237</code> | ||
+ | |||
+ | 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 == | ||
== 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. |
Latest revision as of 12:45, 1 May 2012
This tool has been DEPRECATED, and replaced by Polymutt
|
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.
Basic Usage Example
Here is an example of how glfTrio
works:
glfTrio -f NA19239.chrom20.SLX.glf -m NA19238.chrom20.SLX.glf -c NA19240.chrom20.SLX.glf \ --father NA19239 --mother NA19238 --child NA19240 \ --minMapQuality 30 --minTotalDepth 0 --maxTotalDepth 1000 \ -b YRI.chrom20.SLX.vcf > YRI.chrom20.SLX.log
Command Line Options
Input Files
-f genotype likelihood file Father's GLF-format genotype likelihood file -m genotype likelihood file Mother's GLF-format genotype likelihood file -c genotype likelihood file Child's GLF-format genotype likelihood file
Basic Output Options
-b baseCallFile Specifies the name of the output VCF-format base call file -p threshold The threshold for base calling. Base calls will be made when their posterior likelihood exceeds threshold --reference Positions called as homozygous reference will be included in the output. --verbose Print debug information to the screen
Filtering According to Depth and Map Quality
--minMapQuality threshold Positions where the root-means squared mapping quality falls below this threshold will be excluded. --strict When the map quality is interpreted strictly, all three trio individuals must exceed minMapQuality before a call is made. Without the --strict option, reads for individuals below the threshold are ignored.
--minTotalDepth threshold Positions where the read depth falls below this threshold will be excluded. --maxTotalDepth threshold Positions where the read depth exceeds this threshold will be excluded.
Sample Labels
--father fatherLabel Specifies a label for the male parent, which will be included in the output VCF file --mother motherLabel Specifies a label for the female parent, which will be included in the output VCF file --child childLabel Specifies a label for the child, which will be included in the output VCF file
X Chromosome Variant Calling
--xChr chromosomeName Label for the 'X' chromosome in the GLF file --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)
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
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.