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DEploid-Data-Benchmark-in_silico_lab_mixed_4s

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

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