Sib-pair Command: test flips


ClassAnalysis and data manipulation command
Nametest flips
Arguments map|fasta <file_name>

Compare reference alleles given in locus annotations to those in an external VCF, GFF or FASTA file. The FASTA file must be indexed, ie have a .fai file produced by the samtools faidx program. Results are sent to locstat, so one can keep/drop/undrop on the value of the comparison for each SNP.

The test strand command, by constrast, does not use external information.

Example:

>> test flip map HRC.r1.GRCh37.autosomes.mac5.sites.tab.gz

Reading map file "HRC.r1.GRCh37.autosomes.mac5.sites.tab.gz".

Matched 402320 out of 538448 loci to reference allele data.
Discordance between annotation and reference map at 230693 positions (0.5734).
Excludes discordances at each of 1307 duplicates on reference map.

>> sum tab

Test: "Allele consistency with reference: 0=OK 1=swap 2=incon".

Category     Count
---------- -------
0=OK        171627
1=swap      229741
2=incon        952


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