Running Aellic Expression Imbalance

Running aellic expression imbalance analysis on RNA-Sequencing data. Counts the alleles in the specified bam files from ‘file_to_sample_mapping.txt’ at locations specified in the genotype file. The script returns a pandas dataframe pickled to a file specified by OUTPUT. The columns of the aei dataframe is a multi-index with the first index being the sample id and the second index composing of base pairs in the order as specificed: [A, G, C, T].

:TODO Need to handle indels tag SNPs.

file_to_sample_mapping.txt should have the following tab-delimited format.

‘’’ sample_name path_to_file Sample_1 /proj/data/sample_1.bam ‘’‘

genotype_data is a file specificying which SNPs to count at in the 1000G VCF type format.

At the moment the script has a lot of limitations. Tested on STAR and tophat aligned bams.