From GersteinInfo

Revision as of 16:15, 7 June 2013

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.

Installation

1. Download the tool.
2. Type

$make

Usage

java -Xmx10000m -jar vcf2diploid.jar -id sample_id -chr file1.fa file2.fa ... [-vcf file1.vcf file2.vcf ...] > logfile.txt

OPTIONS:
id          - (required) the ID of individual whose genome is being constructed (e.g., NA12878). The tool recognizes by this ID in the VCF file 

chr         - (required) FASTA file(s) of reference sequence(s) 

vcf         - (required) VCF4.0 file(s) containing variants from parents and the individual 


Xmx         - max memory allocation for JAVA. In this example, 10GB was allocated.
logfile.txt - stores the standard output produce from the run

Output

(a) Maternal and paternal FASTA files
These are the references used for the AlleleSeq pipeline.

(b) Map files
These are coordinate files that correspond the variants on the parental genomes and the reference genome. This is especially important when insertions and deletions are included in the construction of the diploid genome. For instance, there might be an insertion in the reference genome at position 71, not found in the paternal or the maternal haplotype.

(c) Chain files
Using the chain file, one can use the LiftOver tool to convert the annotation coordinates from reference genome to personal haplotypes. This is compatible with the LiftOver tool from UCSC: http://genome.ucsc.edu/goldenPath/help/chain.html

Please refer to the README of vcf2diploid for a more detailed description.

AlleleSeq Pipeline