Create read mapping and variant calling snakefile - Githubissues

dahak-metagenomics / dahak

benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.

https://dahak-metagenomics.github.io/dahak

BSD 3-Clause "New" or "Revised" License

21 stars 4 forks source link

Create read mapping and variant calling snakefile #46

Open brooksph opened 6 years ago

brooksph commented 6 years ago

Expected behavior

Call variants from metagenomic samples using bwf and samtools.

Actual behavior

Steps to reproduce the behavior

brooksph commented 6 years ago

written and working:

[x] Create rule to index contigs
[x] Create rule to convert SAM to BAM
[x] Create rule to sort BAM file
[X] Create rule to Index BAM file
[x] Create rule to create bcf
[x] Create rule to convert bcf to vcf
[x] Create rule to calculate stats
[x] 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/)