This repository contains in silico mixture of 3D7, DD2, HB3 and 7G8, with different mixing proportions.
| 3D7 | DD2 | HB3 | 7G8 | |
|---|---|---|---|---|
| cb_3D7_HB3_DD2_7G8_w1 | .1 | .2 | .3 | .4 |
| cb_3D7_HB3_DD2_7G8_w2 | .25 | .25 | .25 | .25 |
| cb_3D7_HB3_DD2_7G8_w3 | .2 | .2 | .2 | .4 |
| cb_3D7_HB3_DD2_7G8_w4 | .3 | .3 | .3 | .1 |
The script extract VCF columns from wg_vcf/GB4.wg.vcf.gz, and overlap with
lab mixture panels to get the wanted SNP positions. We use HB3.eg.vcf.gz to
provide a total coverage profile, and draw binomial random variables
(alternative allele count) from the total coverage, with given probabilities
(WSAF, adjusted by error 0.01 to mimic sequencing error).
To generate the data:
R CMD BATCH generateLabMixedOf4s.r