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| + | [[Category:Software]] |
| + | {| 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> |
| + | |} |
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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: |
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− | 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 --minTotalDepth 0 --maxTotalDepth 1000 \ |
| + | -b YRI.chrom20.SLX.vcf > YRI.chrom20.SLX.log |
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| == Command Line Options == | | == Command Line Options == |
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| === Basic Output Options === | | === Basic Output Options === |
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− | -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file | + | -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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| --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded. | | --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'' | + | --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.
| + | before a call is made. Without the --strict option, reads for individuals below the threshold are ignored. |
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− | --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. |
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| === Sample Labels === | | === Sample Labels === |
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− | --father ''father label'' Specifies a label for the male parent, which will be included in the output VCF file | + | --father ''fatherLabel'' Specifies a label for the male parent, which will be included in the output VCF file |
− | --mother ''mother label'' Specifies a label for the female 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 ''child label'' Specifies a label for the child, 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 |
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| === X Chromosome Variant Calling === | | === X Chromosome Variant Calling === |
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− | --xChr ''chromosome name'' Label for the 'X' chromosome in the GLF file | + | --xChr ''chromosomeName'' Label for the 'X' chromosome in the GLF file |
− | --xStart ''sex chromosome start'' 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 ''sex chromosome end'' 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) |
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| + | For NCBI genome build 36, you should use the settings <code>--xChr X --xStart 2709521 --xStop 154584237</code> |
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| + | For NCBI genome build 37, you should use the settings <code>--xChr X --xStart 2699520 --xStop 154931044</code> |
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| == Model for Variant Calling == | | == Model for Variant Calling == |
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| == TODO == | | == TODO == |
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| + | Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds. |
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| 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. |