Merge data from SNV, Indel and CNV to create a dataframe with Allelic Count for each mutational position

[shashwatsahay]

Input files required
A config file defining the metadata file and location of genome file

The meta data file is a csv file with the following columns

1. Paitient: A unique identifier to paitient
2. Sample: A unique identifier to sample can be the same over multiple patients
3. Bam file: Bam file for the paitient-sample combination
4. Genomic locations file in bed format: A combined set of mutational locations of SNV or Indels found for all the samples from the same patient
5. CNV file: A CNV file containing the following rows, chr, startpos, endpos, CN
6. Purity: Tumour cell content for the sample
7. Ploidy: Ploidy of the sample

Output:

A tsv per pid contatining the following coulumns

1. Sample ID: A unique identifier for sample fetched from the meta data file
2. ID: A unique Id in the format chr:pos:ref:alt (or any other format but should be unique per sample id)
3. allelic count: computed
4. VAF: computed