Hi, I'm trying to calculate LD for a population. According to this post: http://sourceforge.net/p/vcftools/mailman/message/33219601/, the author says that it should be fine for haploid individuals if their genotype is 1 or "1|.":

Apologies. The announcement was slightly misinformative. The change allowed one to calculate r^2 with genotypes of the form '1|.', but not actually for haploids like '1'. I've just committed a change to allow the second case, so please give it a go and drop me a line if there are any issues.

So I tried calculating LD on my vcf file like so:

vcftools --vcf HA.diploid.vcf --hap-r2 --out test

But I got only nan in my output for the value of r^2. I then converted my VCF to have 1|. for the genotype field instead of just 1 (looks something like this):

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.mpileup.all.snp.vcfsamp.vcf   M-Ait9.22003_GTCTGTCA_C5E9DANXX_6_20140930B_20140930.bam.mpileup.all.snp.vcfsamp.vcf    M-ELH20.18511_ATCCTGTA_C41F2ACXX_6_20140423B_20140423.bam.mpileup.all.snp.vcfsamp.vcf   M-ELH27.18516_CCTCTATC_C41F2ACXX_6_20140423B_20140423.bam.mpileup.all.snp.vcfsamp.vcf   M-ARB0.18513_GCTAACGA_C41F2ACXX_6_20140423B_20140423.bam.mpileup.all.snp.vcfsamp.vcf    M-Set0.22009_CATACCAA_C5E9DANXX_6_20140930B_20140930.bam.mpileup.all.snp.vcfsamp.vcf
1       306     .       G       T       .       PASS    AC=1;AN=1;SF=9  GT      .|.     .|.     .|.     1|.     .|.     .|.
1       375     .       A       G       .       PASS    AC=5;AN=5;SF=1,2,3,9,15 GT      1|.     1|.     .|.     1|.     1|.     1|.
1       424     .       C       A,T     .       PASS    AC=3,0;AN=3;SF=2,6,9,14,15,16,19        GT      .|.     1|.     .|.     1|.     .|.     1|.
1       465     .       G       A       .       PASS    AC=1;AN=1;SF=5,15       GT      .|.     .|.     .|.     .|.     .|.     1|.
1       508     .       T       C       .       PASS    AC=5;AN=5;SF=1,2,3,5,6,9,10,12,14,15,16,17,19,20        GT      1|.     1|.     .|.     1|.     1|.     1|.​

But my output is still nan:

CHR     POS1    POS2    N_CHR   R^2     D       Dprime
1       306     375     1       nan     0       nan
1       306     465     0       nan     nan     nan
1       306     508     1       nan     0       nan
1       306     528     1       nan     0       nan
1       306     711     1       nan     0       nan
1       306     723     1       nan     0       nan
1       306     727     0       nan     nan     nan
1       306     856     0       nan     nan     nan
1       306     864     1       nan     0       nan​

Any ideas on what I'm doing wrong? Thank you very much!