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We will illustrate how TrioCaller works in sequence data including trios and unrelated samples. We will start from the scratch and walk through all necessary steps
We will illustrate how TrioCaller works in sequence data including trios and unrelated samples. We will start from the scratch and walk through all necessary steps
from raw sequence data to called genotypes. If you are new to sequence data, please be patient to go through every step. If you are experienced, you may jump to the section of TrioCaller.
from raw sequence data to called genotypes. If you are new to sequence data, please be patient to go through every step. If you are experienced, you may jump to the section of TrioCaller
[http://genome.sph.umich.edu/wiki/TrioCaller#Genotype_Refinement_Using_Linkage_Disequilibrium_Information].
We will start with a set of short sequence reads and associated base quality scores (stored in a fastq file), find the most likely genomic location for each read (producing a BAM file), generate an initial list of polymorphic sites and genotypes (stored in a VCF file) and use haplotype information to refine these genotypes (resulting in an updated VCF file).
We will start with a set of short sequence reads and associated base quality scores (stored in a fastq file), find the most likely genomic location for each read (producing a BAM file), generate an initial list of polymorphic sites and genotypes (stored in a VCF file) and use haplotype information to refine these genotypes (resulting in an updated VCF file).
