Write

Sometimes one wishes to save a numeric matrix to VCF file. This can be accomplished by the write_vcf function.

using VCFTools
using Random
using Test

Phased genotypes

Let us simulate haplotypes H1 and H2, where each row is a haplotype and each column is a SNP. So Sample 1's gegnotype is H1[1, :] + H2[1, :]. We will save these haplotypes into 0|0, 0|1, 1|0, 1|1 accordingly.

H1 = bitrand(100, 200) # simulated haplotype 1
H2 = bitrand(100, 200) # simulated haplotype 2
write_vcf("test.write.vcf.gz", H1, H2) # write routine

The writen file can of course be re-imported, and we can check that they are the same as H1 and H2:

H = convert_ht(Bool, "test.write.vcf.gz")
@test all(H1 .== view(H, 1:2:size(H, 1), :))
@test all(H2 .== view(H, 2:2:size(H, 1), :))

Test Passed

Unphased genotypes

Similarly, write_vcf can also save unphased genotypes stored in a numeric matrix X. In this case, all heterozygous genotypes will be saved as 1/0.

X = H1 + H2
write_vcf("test.write.vcf.gz", X)

We can also check that the written VCF file is the same as the original after re-importing it

G = convert_gt(Float64, "test.write.vcf.gz")
@test all(G .== X)

Test Passed

# clean up
rm("test.write.vcf.gz", force=true)