Sib-pair Command: test vcf


ClassAnalysis and data manipulation command
Nametest vcf
Arguments <map_file> [ped_id].

Compare genotypes for the matching IDs and loci in current dataset to those in the specified VCF file. Flips strand as necessary.

Results of the comparison are stored as locstat values:

-1Not comparable (different alleles)
1..NNumber concordant at that locus

Example:

>> read bin current.bin.gz
>> test map matching.vcf.gz

Comparing current map to "matching.vcf.gz".
No. INFO vars  = 0 ()
     Duplicate match rs112159604 17:33680507 rs112159604 17:33768734
     Duplicate match rs1044307 X:2404619 rs1044307 Y:2354619

Number of markers Sib-pair map  = 366087
Number of markers external map  = 414450
Total number intersecting       = 45059 (0.123, 0.109)
Intersecting on marker name     = 41955 (discordant position=2)
Intersecting on map position    = 45057 (discordant name=3104)
Number where multiple matches   = 2
Number unique to Sib-pair map   = 321028

>> test vcf matching.vcf.gz

Comparing VCF genotype data on ID string of form "ped_id":

VCF file                        = matching.vcf.gz
File format                     = "VCFv4.1"

Individuals genotyped in VCF file = 62
VCF IDs matching current dataset  = 60
Proportion of dataset updatable   = 0.0310

[...]

NOTE: Inconsistent alleles between current dataset (AG) and VCF file (GC) for "rs139571477".
NOTE:  Current map has "rs1044307" at chrX:2404619 but VCF file has chrY:2354619

Total number of loci scanned    = 414450
Number of matched loci          = 42652 (10.3%)
Number of concordant genotypes  = 2427342 ( 94.6%)

Individual                Discordant genotypes
------------------------- --------------------
                 001--001 13825 / 41128 0.3361
                 002--002 13769 / 41157 0.3345
                 003--003 2131 / 41235 0.0517
                 004--004 2049 / 41150 0.0498
[...]
               0010--0010 1981 / 42243 0.0469

>> sum tab

Test: "Number of concordant genotypes in VCF file".

Category     Count Percent
---------- ------- -------
   -1           23     0.1
    0           37     0.1
    1           31     0.1
    2           26     0.1
    3           34     0.1
[...]
   59         3733     8.8
   60        28989    68.0

>> set plevel 2
>> test vcf matching.vcf.gz

[...]
NOTE:  Genotype at "rs2272757" for 00022--00022 VCF=  G/G   dataset=  A/A
[...]


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