Implement version 1 of an allele specific expression function

[malachig]

Inputs:

• Transcriptome GTF file
• somatic VCF (SNVs)
• germline VCF (SNPs). This could be germline calls from the individual or simply a dbSNP VCF. To be this flexible we need to actually check for heterozygous status in the patient.
• tumor RNA-seq BAM
• tumor DNA BAM

We are looking for somatic SNVs that occur near a locus that has a SNP that is heterozygous in the tumor DNA but expression of the SNP in the RNA is not heterozygous.

Outputs:

• One result for each heterozygous SNP position that is within a known transcript(s) where that transcript also has a somatic heterozygous SNV within some neighborhood (user configurable).

[malachig]

Called regtools cis-expression-effects identify ?

[malachig]

Determine relevance of this tool for this task:

GATK ASEReadCounter

https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_rnaseq_ASEReadCounter.php

[gatoravi]

cis-ase identify is now a module