Sequence allele read counts

Format

There are two lines per individual. The first line gives the individual’s ID and allele read counts for the reference allele at each locus. The second line gives the individual’s ID and allele read counts for the alternative allele at each locus.

The same format works for the autosomes and the X chromosome. Only loci on one chromosome should be provided!

Example with four individuals and their allele read counts at four loci:

id1 4 0 0 7 # Reference allele read counts for id1
id1 0 3 0 0 # Alternative allele read counts for id1
id2 1 3 4 3
id2 1 1 6 2
id3 0 3 0 1
id3 5 0 2 0
id4 2 0 6 7
id4 0 7 7 0

Input details

If provided, values from this file are translated to the penetrance component of genotype probabilities. The file does not need to include all individuals present in other files. Only loci on one chromosome should be provided!