3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
[[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>
|}
'''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.
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
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 ===
--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.
