# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>

# <markdowncell>

# - Start copying over Pf 4.0 vcf (currently running)
# - Start copying over bam files for all samples (20150605_transfer_bams.ipynb)
# - Figure out how to pull out relevant rows from vcf, e.g. by creating a bed (samtools?)
# - Missingness per sample plots (broken down by Pf, human, water)
# - Missingness per assay plots (broken down by Pf, human, water)
# - Discordance table
# - Discordance by sample and by assay plots
# - Cluster plots, coloured by Sequenom calls, Christina calls and Illumina calls
# - Colour cluster plots by Pf, human, water, dilution
# - Add lines to cluster plots (to recreate Kirk's)
# - Comparison of allelic ratio plots
# - New calling based on different thresholds, including concordance
# 
# - Analysis of previous Christina calls, including different thresholds on different plates
# - Can we make an argument for same thresholds on different plates?

# <codecell>


