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tss101  committed e08424c

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 opticall reads in file of intensity data (currently Illumina normalized intensities) and clusters them considering both per-SNP and per-sample information, and provides genotype calls as output. The intensity input file is tab separated, with SNPs are rows, and samples as columns. So a line would be: 
 
-rsid<tab>rscoord<tab>allelesAB<tab>id_1A<tab>id_1B<tab>id_2A<tab>id_2B etc.
+rsid<tab>rscoord<tab>allelesAB<tab>id1A<tab>id1B<tab>id2A<tab>id2B etc.
 
-where id_1A is the allele A intensity value for sample 1, and id_1A is the allele B intensity value for sample 1. The algorithm is known to perform well with Illumina normalized intensities. Any missing intensities should be input as NaN for both the A and B alleles.
+where id1A is the allele A intensity value for sample with id id1, and id1B is the allele B intensity value for sample 1. The algorithm is known to perform well with Illumina normalized intensities. Any missing intensities should be input as NaN for both the A and B alleles.
 
 The first line of the file should also be a header line of the form: