Mapper: Call variants (BAM -> VCF)

[eweitz]

In the Mapper module, supporting taking BAM input data and converting it to VCF output.

@dauss75, @chris-owen, this is one of the issues we discussed.

[chris-owen]

Here is the pipe to generate a quality filtered VCF file from a BAM file. The example below generates the the VCF using Freebayes and filters the VCF by quality score (e.g., phred 30).

/home/ubuntu/freebayes/bin/freebayes -f /home/ubuntu/refs/fasta/GCF_000001405.30_GRCh38.p4_genomic.fna <dummy.bam> | /home/ubuntu/vcflib/bin/vcffilter -f "QUAL > 30" > results.vcf