sdentro / targeted_het_snp_imbalance

Pipeline to call significant imbalance of heterozygous SNPs

Mouse heterozygous SNP imbalance pipeline

For targeted sequencing data

Running

First make sure to place all BAM files in the raw_data directory

Then add samples to the sample_mapping.txt file. This file contains two columns, separated by a tab: samplename and controlsamplename

Please note that samplenames must be unique. The name provided in sample_mapping.txt is used to pattern match BAM files and output of the pipeline

hg19

Run in this order:

• allelecount
• phasing
• combine
• plotting

mm10

Run in this order:

• allelecount
• segmentation
• combine
• plotting

Dependencies - overall

• alleleCounter
• R
• optparse
• Battenberg
• ggplot2
• gridExtra
• gtools
• GenomicRanges

hg19 - additional dependencies

• Impute2

Reference data

hg19

Reference data to count alleles and perform haplotype reconstruction is available on the Battenberg github page

• Battenberg GRCh37 reference files from here

mm10

First download the SNP reference data from the mouse genomes project here: ftp://ftp-mouse.sanger.ac.uk/current_snps

Then cd reference and check the correct filename is referenced in split.sh.

Finally run ./split.sh, which takes a while to generate the alleles