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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 ==
