Update fastq2vcf script according to mitolin plan

## Background

At the beginning of this project, Kerrigan Blake gave us her sequence processing script that was run with gatk 4.0.0.0. The current version of gatk is 4.1.2.0 (as of 08/5/2019). There are numerous differences between version 4.0 and 4.1.

## Aim

Create script mitolin/src/fastq2vcf-gatk-v0.1.0.sh using the [mitolin plan](https://github.com/deepcelllineage/overview/wiki/mitolinplan-v0).

Run the script to generate vcf files.

Also run the mitolin/src/vcf2fasta_v0.2.0.sh script to make fasta sequences.

Maybe add vcf to fasta as an extra command in the fastq2vcf script.