vtools_report inbreeding_coefficient calculates the \(F\) statistic at single individual sample level from genotype data. It measures the reduction in heterozygosity for given genomic region of samples, compare to expected heterozygosity level under Hardy-Weinberg Equilibrium. For a two allelic locus, $$P(AA)=p^2(1-F)+pF$$$$P(aa)=q^2(1-F)+qF$$$$P(Aa)=2pq(1-F)$$We compute estimate for \(F\) as \(\hat{F}=1-\frac{#observed(Aa)}{#expected(Aa)}\)
Variants included for calculation of \(F\) must be under HWE and be bi-allelic. Tri-allelic loci are automatically excluded from calculation.
Estimate of MAF using given samples should be computed prior to calculation of \(F$, via vtools update TABLE --from_stat <em>maf=maf()</em>.
vtools_report inbreeding_coefficient -h
usage: vtools_report inbreeding_coefficient [-h]
[--samples [SAMPLES [SAMPLES ...]]]
--maf_field MAF_FIELD [-v {0,1,2}]
table
Report F statistic which describe the expected degree of a reduction in
heterozygosity when compared to Hardy-Weinberg expectation. In simple two
allele system with inbreeding, P(AA) = p^2(1-F)+pF, P(aa) = q^2(1-F)+qF and
P(HET) = 2pq(1-F). For an individual F is estimated by F = 1 - #observed(HET)
/ #expected(HET). Tri-allelic loci, if identified, are excluded from
calculation.
positional arguments:
table Variants based on which individual inbreeding
coefficients are evaluated.
optional arguments:
-h, --help show this help message and exit
--samples [SAMPLES [SAMPLES ...]]
Conditions based on which samples are selected to have
inbreeding coefficients calculated. Default to all
samples.
--maf_field MAF_FIELD
Name of the field that holds minor allele frequency
for sample variants, which is the field name for
command 'vtools update table --from_stat
"maf_field=maf()" --samples ...'.
-v {0,1,2}, --verbosity {0,1,2}
Output error and warning (0), info (1) and debug (2)
information of vtools and vtools_report. Debug
information are always recorded in project and
vtools_report log files.
Compute MAF for given samples
vtools update variant --from_stat 'mafEUR=maf()' --samples "super_pop='EUR'" -j8
We evaluate heterozygosity level on chromosome 1
vtools select "chr='1'" -t chr1
Inbreeding coefficients are computed and saved to file chr1.inbreeding.txt
vtools_report inbreeding_coef chr1 --maf_field mafEUR --samples "super_pop='EUR'" > chr1.inbreeding.txt
HG00118 0.00599944241381
HG00119 0.00206096581669
HG00120 0.0114070032711
HG00121 0.0461496321201
HG00122 0.0127749763012
HG00123 0.00582167049467
HG00124 0.0129693670104
...