Genotype information for a variant is not directly available in variant tools commands such as vtools output because these commands only output variant info or annotation fields. Function genotype can be used to retrieve genotypes of one or more samples from the genotype tables. In its single-sample mode, this function accepts a sample name and an optional field to display,
genotype(sample_name, params='')
where params can have be multiple parameters joined by &. For example, functions
genotype('WGS1')
genotype('WGS1', 'field=DP')
returns the genotype (0 for homozygous wild type, 1 for heterzygous alternative, 2 for homozygous alternative, and -1 for one of the double alternative alleles) or genotype field DP of sample WGS1. '.' will be returned if sample WGS1 does not contain the variant.
Let us get a simple project and name the samples properly
% vtools admin --load_snapshot vt_simple
% vtools admin --rename_samples "filename='V2.vcf'" SAMP2
% vtools admin --rename_samples "filename='V3.vcf'" SAMP3
% vtools show samples
sample_name filename
SAMP1 V1.vcf
SAMP2 V2.vcf
SAMP3 V3.vcf
There are about 1000 genotypes in three samples:
% vtools show genotypes
sample_name filename num_genotypes sample_genotype_fields
SAMP1 V1.vcf 989 GT
SAMP2 V2.vcf 990 GT
SAMP3 V3.vcf 988 GT
Now, in addition to the variant inforation, we would like to see the genotype of variants in sample SAMP1
% vtools output variant chr pos ref alt "genotype('SAMP1')" -l 10
1 4540 G A 1
1 5683 G T 1
1 5966 T G 1
1 6241 T C 1
1 9992 C T 1
1 9993 G A 1
1 10007 G A 1
1 10098 G A 2
1 14775 G A 2
1 16862 A G 2
The genotype can also be used to select variants. For example, the following command select variants when their genotypes in SAMP1 is heterzygous. When we output genotypes of these variants in two samples, some of them are not available in SAMP2 and are displayed as missing (.).
% vtools select variant "genotype('SAMP1')=1" --output chr pos ref alt \
"genotype('SAMP1')" "genotype('SAMP2')" -l 10
1 4540 G A 1 .
1 5683 G T 1 .
1 5966 T G 1 1
1 6241 T C 1 .
1 9992 C T 1 .
1 9993 G A 1 .
1 10007 G A 1 1
1 20723 G C 1 1
1 29539 C T 1 .
1 39161 T C 1 .
In addition to genotype, you can use the genotype() funciton to display other genotype info fields (c.f. vtools show genotypes, for example, for a project with genotype info field DP_geno, we can specify name of the genotype info field as a second parameter:
% vtools init genotype -f
% vtools import CEU.vcf.gz --geno_info DP_geno --build hg18
% vtools output variant chr pos ref alt "genotype('NA12874')" "genotype('NA12874', 'field=DP_geno')" -l 10
1 533 G C 1 9
1 41342 T A 0 3
1 41791 G A 0 2
1 44449 T C 0 0
1 44539 C T 0 0
1 44571 G C 0 0
1 45162 C T 0 1
1 52066 T C 1 3
1 53534 G A 0 0
1 75891 T C 0 0
The first parameter can also be a condition based on which several samples are selected (default to all samples). In this case, this function will return a list of genotypes (for default field='GT') or other fields. Two additional parameters are acceptable (joined by &):
delimiter: Delimiter, defalt to ,.missing: If a sample does not contain the variant, output this string instead of ignoreing the sample.For example, functions
genotype()
genotype('aff=1')
genotype('BMI>20', 'field=DP_geno&missing=.')
returns genotypes of all samples, samples with aff=1, and depth of coverage of of all samples with BMI > 20, respectively.
% vtools init genotype -f
% vtools import CEU.vcf --geno_info DP_geno --build hg18
% vtools remove genotypes 'GT=0'
% vtools output variant chr pos ref alt "genotype()" -l 10
1 533 G C 1,1,1,1,1,1
1 41342 T A 1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,2,1,1,1,1,1,2,1,1,1
1 41791 G A 1,1,1,1,1
1 44449 T C 1,1
1 44539 C T 1,1
1 44571 G C 1,1,1,1,1,1,1
1 45162 C T 1,2,1,1,1,1,2,1,1,1,1,2,1,1,1,2
1 52066 T C 1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1
1 53534 G A 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
1 75891 T C 2,1,2,1,1,1,2,1
If you would like to limit the samples, you can pass a condition (c.f. vtools show samples)
% vtools phenotype --from_file phenotype.txt
% vtools output variant chr pos ref alt "genotype('BMI>24')" -l 10
1 533 G C .
1 41342 T A 1,1
1 41791 G A 1
1 44449 T C .
1 44539 C T .
1 44571 G C 1,1,1
1 45162 C T 1
1 52066 T C 1,1
1 53534 G A 1
1 75891 T C 2
If you need to know which samples have these genotypes, you can use function samples() with the same condition.
% vtools output variant chr pos ref alt "samples('BMI>24')" -l 10
1 533 G C .
1 41342 T A NA11918,NA12814
1 41791 G A NA11918
1 44449 T C .
1 44539 C T .
1 44571 G C NA12003,NA12287,NA12751
1 45162 C T NA12814
1 52066 T C NA12003,NA12751
1 53534 G A NA12287
1 75891 T C NA12814
Using strings inside the condition is bit tricky because you need to use backslash to pass condition sex='F' to the genotype function in the following example:
% vtools output variant chr pos ref alt "genotype('sex=\'F\'')" -l 10
1 533 G C 1,1,1,1
1 41342 T A 1,1,1,1,1,1,1,1,2,1,1,1,1,1
1 41791 G A 1,1,1
1 44449 T C 1,1
1 44539 C T 1,1
1 44571 G C 1,1,1,1,1
1 45162 C T 1,2,1,1,2,1,1,1,1,1
1 52066 T C 1,1,1,1,1,1,1,1,1
1 53534 G A 1,1,1,1,1,1,1,1,1,1,1,1,1,1
1 75891 T C 2,1,2,1,2
Finally, if you would like to view values of other genotype info fields (c.f. vtools show genotypes), or using alternative delimiters, you can
% vtools output variant chr pos ref alt "genotype('BMI>23', 'field=DP_geno&d=\t&missing=.')" -l 10
1 533 G C . . . . . . . . . .
1 41342 T A . 1 4 3 . . . . 0 9
1 41791 G A . 2 . . . . . . . .
1 44449 T C . . . . . . . . . .
1 44539 C T . . . . . . . . . .
1 44571 G C . . . . 1 1 4 1 . .
1 45162 C T 4 . . . . . . . . 7
1 52066 T C . . 3 . 1 . . 1 . .
1 53534 G A 5 . . . . . 5 . . .
1 75891 T C . . . . . . . . . 6
Whereas the return value of genotype(sample_name) is an integer, the return value of genotype(sample_cond) is always a string, evern if only one sample is selected by the condition.
You could match returned genotypes with samples by comparing the output of genotype(sample_cond) with the output of samples(sample_cond).