Basic Usage Example
Here is an example of how
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
-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.
--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
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.