The is a new version for the script to create bin markers. Previous version: BinMarkers
- Author: Leiting Li
- Email: lileiting@gmail.com
- LICENCE: BSD
USAGE
binmarkers-v2.3.pl [Options] <input.markers.txt>
Description
Asssume the input data is a tab-seperated matrix,
with first line as title [optional] and first column as marker name.
Markers name format: scaffold_start:end:markers.
For example, scaffold0001_10:10000:10 means a bin markers
spanned scaffold0001, from 10 bp to 10000 bp, included
10 original markers.
Assume genotypes were encoded as a, A, b, B, h, H, `-`, u, `.`, `..`, `--`.
A is equivalent to a; B is equivalent to b;
H is equivalent to h; `u`, `--`, `.`, `..` are equivalent to `-`.
This protocol required five main steps:
1. Bin markers by 10 kb window using majority rules [-m 1 -w 10_000]
2. Fill missing genotypes using majority rules:
round 1: [-m 2 -w 3]
round 2: [-m 2 -w 5]
round 3: [-m 2 -w 7]
3. Fill missing genotypes by in the breakpoints [-m 3 -w 3]
4. Correct misscored genotypes with strict criteria [-m 4 -w 5]
5. Merge 100% identical markers [-m 5]
* Step 2 and step 4 will process the first and last [w] markers
Majority rules ([w] markers above, [w] markers below):
if two genotypes were equal weights, treat as missing data
Strict criteria for correcting misscored genotypes:
A genotype is different with surroundings genotypes;
No missing data in surroundings genotypes;
Surroundings genotypes are the same.
Example commands:
perl binmarkers-v2.3.pl example.input.markers.txt -m bin -w 10_000 -o out.step1.txt
perl binmarkers-v2.3.pl out.step1.txt -o out.step2.1.txt -m fill -w 3
perl binmarkers-v2.3.pl out.step2.1.txt -o out.step2.2.txt -m fill -w 5
perl binmarkers-v2.3.pl out.step2.2.txt -o out.step2.3.txt -m fill -w 7
perl binmarkers-v2.3.pl out.step2.3.txt -o out.step3.txt -m fill2 -w 3
perl binmarkers-v2.3.pl out.step3.txt -o out.step4.txt -m correct -w 5
perl binmarkers-v2.3.pl out.step4.txt -o out.step5.txt -m merge
Or use pipe to run them in one command, such as
perl binmarkers-v2.3.pl example.input.markers.txt -m bin -w 10_000 |
perl binmarkers-v2.3.pl -m fill -w 3 |
perl binmarkers-v2.3.pl -m fill -w 5 |
perl binmarkers-v2.3.pl -m fill -w 7 |
perl binmarkers-v2.3.pl -m fill2 -w 3 |
perl binmarkers-v2.3.pl -m correct -w 5 |
perl binmarkers-v2.3.pl -m merge -o out.step5.txt
For manual checking, just copy data in the `example.input.markers.txt` file
and the `out.step4.txt` file in an Excel file and then sort by
marker names
OPTIONS
-t, --title Treat first line as title [default: no title line]
-w, --window NUM Window size [defaults are based on differnt modes]
-m, --mode NUM Select modes:
bin: Bin markers for a larger block [default: -w 10_000]
fill: Fill missing data (majority rules) [default: -w 3]
fill2: Fill missing data in the breakpoints [default: -w 3]
correct: Correct misscored genotypes [default: -w 5]
correct2: Correct misscored genotypes [default: -w 5]
correct3: Correct misscored genotypes [default: -w 5]
merge: Merge adjacent 100% identical markers
-o, --out FILE Output file [default: stdout]
--no_edge Do not process the first and last [w] markers,
valid to -m 2 and -m 4
--minimum NUM Minimum block size for -m 2 and -m 4
[default: (w) * 2 + 1]
-h, --help Print help
When using this program please cite the following paper:
Qin M-F, Li L-T, Singh J, Sun M-Y, Bai B, Li S-W, Ni J-P, Zhang J-Y, Zhang X, Wei W-L, Zhang M-Y, Li J-M, Qi K-J, Zhang S-L, Khan A, Wu J. Construction of a high-density Bin-map and identification of the fruit quality related quantitative trait loci and functional genes in pear. Horticulture Research, 2022, uhac141.