Documenting vcf_filtration - Githubissues

raikens1 / mutation_rate

Code and raw data files for my work on private polymorphism differences between populations.

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Documenting vcf_filtration #5

Open raikens1 opened 6 years ago

raikens1 commented 6 years ago

Write shell scripts that do the following

[x] Filter 1kg vcf files based on required regions/params
[x] Intersect two populations (just an example script might be a good start - add this to priv_multiallelic)
[x] Run counter on all chromosomes for a given POP and kmer.
[ ] Make a graphic that shows visually the pipelines I've used for filtration and the scripts that do that.

We also need

[ ] Figure out what items need to go on the github. Perhaps nothing. just add a folder with sample scripts and a very detailed README
[x] Edit the Readmes in the AMR directory so they more closely resemble the template used in the READMEs for other pops.

raikens1 commented 6 years ago

Moved count_all_7mers,sh to helper_code. It will need some work before it is more generally usable. I want to set it up so it takes an argument for kmer. Also will need to change it around a bit once I get counter set up to run with an input chromosome.