Create read mapping and variant calling snakefile

[brooksph]

Expected behavior

Call variants from metagenomic samples using bwf and samtools.

Actual behavior

Steps to reproduce the behavior

[brooksph]

written and working:

• Create rule to index contigs
• Create rule to convert SAM to BAM
• Create rule to sort BAM file
• Create rule to Index BAM file
• Create rule to create bcf
• Create rule to convert bcf to vcf
• Create rule to calculate stats
• Create rule to filter variants

debugging:

• Create rule to map reads to contigs
  • Encountering error when running on subsampled datasets
    [mem_sam_pe] paired reads have different names: "SRR606249.1.", "SRR606249.32014193."

to do:

• Determine best method for visualization
  • We may punt this to OY or 2.0 release. Alternatively, a good option is something similar to what anvio does http://merenlab.org/2015/07/20/analyzing-variability/ .
• Create snakefile to link snakefiles
  • http://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#includes

Notes:

• Determine if indexing and subsequent steps should be combined or find a way to point to indexed files.
• In newer versions variant calling can be done with bcf mpileup and bcf call (no longer samtools mpileup and alone (see http://www.htslib.org/workflow/)