533
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Example Dataset
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).
== Example Dataset ==
=== Example Dataset ===
Our dataset consists of 40 individuals, which have been sequenced at an average depth of 3x.
Our dataset consists of 40 individuals, which have been sequenced at an average depth of 3x.
