Sequence allele read counts file

Input file

This file has two lines with observed allele read counts for each sequenced individual. The file does not need to include all individuals present in other files. The first line gives the individual’s ID and 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