AlleleSeq
From GersteinInfo
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.
