File formats
summary file
The summary file is ASCII encoded. It consists of two sections—the header and the data. Lines MUST be terminated in the Unix style with a new line (aka line feed) character. Lines in the header section MUST be prefixed with #.
The first line of the header section MUST be # pyhegp summary file version 1. Subsequent lines of the header section are a list of key-value pairs. Each line MUST be #, optional whitespace, the key, a single space character and then the value. The key MUST NOT contain whitespace or control characters, and MUST NOT begin with a # character. The value MAY contain whitespace characters, but MUST NOT contain control characters.
The data section is a tab-separated table of numbers. The first line MUST be a header with column labels. Each row corresponds to one SNP. The columns labelled chromosome, position, reference, mean and standard-deviation contain the chromosome, the position of the SNP on the chromosome, the reference allele, the mean dosage and the standard deviation of the dosage for that SNP. Column labels are case-sensitive.
The reference column is optional, and SHOULD be absent in pooled summary files.
Here is an example summary file.
# pyhegp summary file version 1
# number-of-samples 100
chromosome position reference mean standard-deviation
chr11 3200246 G 0.1677 0.3915
chr11 3205355 T 0.1766 0.3599
chr11 3218908 A 0.1818 0.3169
chr11 3414044 A -0.2420 0.1606
chr11 3460427 C -0.2408 0.1593
chr11 3462290 A -0.2383 0.1670
chr11 3462323 A -0.2388 0.1653
chr11 3462325 T -0.2386 0.1658
chr11 3462348 T -0.2371 0.1702
chr11 3464016 A -0.2400 0.1623
genotype file
The genotype file is a tab-separated values (TSV) file. The first line MUST be a header with column labels. Each row corresponds to one SNP. The columns labelled chromosome, position and reference contain the chromosome, the position on the chromosome and the reference allele for that SNP. Other columns each contain dosage values for one sample. The headers of these columns MUST be their sample identifiers. Column headers are case-sensitive.
the reference column is optional, and should be absent in encrypted genotype files.
Here is an example genotype file.
chromosome position reference sample1 sample2 sample3 sample4
chr11 3200246 G 0.4043 0.3655 0.3375 -0.614
chr11 3205355 T 0.395 0.3545 0.3325 -0.5421
chr11 3218908 A 0.3977 0.3207 0.3134 -0.4491
chr11 3414044 A -0.3616 -0.328 -0.3234 0.074
chr11 3460427 C -0.341 -0.3363 -0.3346 0.073
chr11 3462290 A -0.3552 -0.3281 -0.3287 0.0912
chr11 3462323 A -0.3524 -0.3296 -0.3298 0.0874
chr11 3462325 T -0.3533 -0.3291 -0.3294 0.0885
chr11 3462348 T -0.361 -0.3244 -0.326 0.0986
chr11 3464016 A -0.3461 -0.334 -0.3331 0.08
key file
The key file is a tab-separated values (TSV) file with numerical data. There MUST be no column headers.
Here is an example key file.
-0.4397501 0.37277363 0.63142739 0.50129352 -0.13290571
0.13568008 -0.13505327 0.2149694 -0.29304762 -0.91173613
0.52289655 0.83464826 0.010733899 -0.17227947 0.012084877
-0.70250368 0.31764876 -0.19654188 -0.60576289 -0.0032338057
-0.14587165 0.21274863 -0.71857058 0.51594477 -0.38848011