GlfTrio

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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.