AlleleSeq
From GersteinInfo
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| + | Essentially, it constructs a personal genome integrating the the variants from the parents and child to the reference genome. | ||
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| + | USAGE: | ||
=AlleleSeq pipeline= | =AlleleSeq pipeline= | ||
Revision as of 15:57, 7 June 2013
Contents |
General outline of pipeline
The basic goal of the pipeline is to take a large collection of reads generated from ChIP-seq or RNA-seq experiments associated with an individual and detect single nucleotide variants (SNVs) that correspond to significantly skewed number of reads. To do this, the pipeline starts with a preprocessing step, before the actual process.
(1) Pre-processing - diploid genome construction using vcf2diploid
In the Rozowsky et al. (2011) paper, the
pre-processing step separate (phase) the child's diploid genome into its parental
haplotypes based on the sequences of the parents.
(2) AlleleSeq pipeline - mapping and statistical testing using PIPELINE.mk package
a) Reads from ChIP-seq and RNA-seq experiments are aligned and mapped to both
haplotype genomes.
b) Then for each SNV position with mapped reads, we compare the allele
frequencies observed in the two parental haplotypes.
vcf2diploid
Essentially, it constructs a personal genome integrating the the variants from the parents and child to the reference genome.
USAGE:
