[Vcftools-help] Request help on OUTPUT OTHER STATISTICS --het (Calculates a measure of heterozygosity)

[Dharmendra G. <dha...@eg...>]

Hello,
I am working on Pigs whole genome date from several different species and
at the same time they belong to several different generations(G0, G1, G2,
G3, G4), we are trying to calculate how inbred these pigs are? This will
also tell us how close these pigs are genetical to each other. For this I
am trying VCFtools OUTPUT OTHER STATISTICS --het option, which does say it
calculate heterozygosity but what we get as an output is the calculation of
observed vs expected homozygous and inbreeding coefficient.

vcftools --vcf input_file.vcf --het --out output_het

If you don’t mind can you please let us know if this option --het
application on VCF file is the best way to understand how inbred and close
genetically particular animals are using variants VCF? Or do you have any
other suggestions/advice to get this number? Another question on -het
output, What we get as inbreeding coefficient number range from -0.62854 to
0.67488. The number closer to positive 1 is more inbred than the number
which goes to zero or below. Is negative number indicated toward
heterogeneity in the samples. Another question on N_sites, In VCF file we
have more than several million SNPs and Indels (approx. 12 million) but we
only see close to one and half million in N_sited, do you have any idea how
the N_sites number come from and how the N_sited are filtered from the
input VCF files.

Please also point to the right reference you used for --het calculation
that will be very helpful.

Thanks

Dharm

-- 
*Dharmendra Goswami, PhD *
Computational Biologist
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