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[[Category:Software]]
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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.
--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 <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.
