Sib-pair Command: test map


ClassAnalysis and data manipulation command
Nametest map
Arguments [(merge [<thresh>]) | <map_file>].

Test for multiple loci declared to have the same map position. If the merge modifier has been specified, Sib-pair will merge the genotype data for the two loci is the allelic spectrum is compatible ie same alleles, or compatible with a strand mixup (see the test strand). If too many incompatibilities between genotypes at the same individual are detected (defaul threshold 0.005), then the merge will not proceed.

The duplicate loci are identified by a locstat value > 1, accessible using the summary and drop commands.

If a file name is specified, the current map is compared to that contained in that file, which is read as if by read map. That is, heuristics are used to work out the most likely locus or map file format.

Results of the comparison are stored as locstat values:

0Not compared
1Match on name but not position
2Match on position but not name
3Complete match
4Multiple matches in external map file

Concordance for map position is privileged over locus name in the summary counts (see below for an example)

Example:

>> set loc snp1 snp 1:100
>> set loc snp2 snp 1:100
>> test map
Number of markers placed on map = 2
Number of unplaced markers      = 0
Marker order                    = Map Order
Duplicated map positions        = 1

Chr     Position  Count
--- ------------ ------

>> sum

Test: "map position duplicates".

Total number of tests = 2

Locus              Chr Position   Statistic
------------------ --- ---------- -----------
snp2                1  100.000000    2.000     
snp1                1  100.000000    1.000     

>> drop where test > 1.

Comparing two maps - two SNPs have had their map positions swapped.

>> clear >> set loc rs1815606 mar 1:1.140435 >> set loc rs12565286 mar 1:0.785050 >> set loc rs2905062 mar 1:0.721290 >> set ple 2 >> test map small.vcf Comparing current map to "small.vcf". 1: ##fileformat=VCFv4.0 Reading as a VCF file. No. INFO vars = 4 (TOP_STRAND ALLELEA ALLELEB FLANKPOS) Status Locus Position ExternalName ExternalPosition Discordant name rs2905062 1:721290 rs12565286 1:721290 Discordant name rs12565286 1:785050 rs2905062 1:785050 Complete match rs1815606 1:1140435 rs1815606 1:1140435 Number of markers Sib-pair map = 3 Number of markers external map = 3 Total number intersecting = 3 (1.000, 1.000) Intersecting on marker name = 1 (discordant position=0) Intersecting on map position = 3 (discordant name=2) Number where multiple matches = 0 Number unique to Sib-pair map = 0 >> sum Test: "map comparison". Total number of tests = 3 Locus Chr Position Statistic ------------------ --- ---------- ----------- rs1815606 1 1.140435 3.000 rs2905062 1 0.721290 2.000 rs12565286 1 0.785050 2.000


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