call_windows¶
The gamtools call_windows
tool determines which genomic regions were present in each NP.
The input file is a tab delimited table in which the first three columns indicate the
genomic region in bed format (chrom, start, stop) and the remaining columns give the number
of reads mapping to each genomic region for each NP. For example:
chrom start stop NP_1 NP_2 NP_3 NP_4 NP_5
chr19 0 50000 0 0 0 0 0
chr19 50000 100000 1 26 1 54 0
chr19 100000 150000 0 34 0 0 1
chr19 150000 200000 2 16 0 0 0
chr19 200000 250000 0 1 32 7 0
chr19 250000 300000 3 0 0 0 1
chr19 300000 350000 1 4 50 12 0
chr19 350000 400000 2 3 32 1 3
chr19 400000 450000 0 0 115 0 0
This type of coverage table can be generated quite easily using bedtools multicov and is generated automatically by the GAMtools process_nps command.
The output file is in the same format, but each entry is either a 1 (indicating the region was present) or a 0 (indicating that it was absent).
chrom start stop NP_1 NP_2 NP_3 NP_4 NP_5
chr19 0 50000 0 0 0 0 0
chr19 50000 100000 0 1 0 1 0
chr19 100000 150000 0 1 0 0 0
chr19 150000 200000 0 1 0 0 0
chr19 200000 250000 0 0 1 0 0
chr19 250000 300000 0 0 0 0 0
chr19 300000 350000 0 0 1 1 0
chr19 350000 400000 0 0 1 0 0
chr19 400000 450000 0 0 1 0 0
Usage and option summary¶
Usage:
gamtools call_windows [OPTIONS] <COVERAGE_TABLE>
Optional parameters:
Option | Description |
---|---|
-d, –details-file | Write a table of fitting parameters to this path |
-o, –output-file | Output segregation file to create (or “-” to write to stdout), default is stdout |
-f, –fitting-folder | Save plots for each individual curve fitting to this folder |