
# Cortex_var only compiles and runs cleanly on Linux
# Dependcies: Cortex_var, vcf-hack, stampy, vcftools

Simulate a diploid with 60X coverage (30X per chrom). 1% seq error and
100bp read length, with paired end reads (insert length ~250bp, stddev = 50).

Diploid is simulated by mutating a ref twice to create two chromosomes. We then
call variants with the bubble caller including the reference. Comparing against
the truth gives us a FDR and sensitivity measurement.

Run simulation with k=21 and k=31:

    make K=21 run-mccortex run-cortex >& results/20150428.tues.k21.linux.txt
    make K=31 run-mccortex run-cortex >& results/20150428.tues.k31.linux.txt

Re-run again with read lengths of 150bp:

    make K=21 run-mccortex run-cortex >& results/20150429.wed.k21.linux.txt
    make K=31 run-mccortex run-cortex >& results/20150429.wed.k31.linux.txt

Clean with:

    make clean K=21
    make clean K=31
