Pileup2singledose
A procedure to call single dose SNP from pileup format
- Author: Lei-Ting Li
- Email: lileiting@gmail.com
- LICENCE: BSD
Installation
git clone https://github.com/lileiting/Pileup2singledose.git
How to use it
First step, create a pileup matrix
perl create_pileup_matrix.pl -m male.pileup -f female.pileup -p progeny1.pileup,progeny2.pileup,progeny3.pileup -o pileup.matrix.txt
Second step, call single dose
perl pileup2singledose.pl pileup.matrix.txt > genotypes.matrix.txt
Third step, filter results
perl filter_genotypes.pl -i genotypes.matrix.txt -t 0.2 -o genotypes.matrix.t0.2.txt
Fourth step, convert genotypes codes from h, a, b to lm, ll, nn, np
perl convert_genotypes.pl genotypes.matrix.t0.2.txt > genotypes.matrix.t0.2.cp.txt
Fifth step, convert format for BinMarkers
perl format4binmarkers.pl genotypes.matrix.t0.2.cp.txt > genotypes.matrix.t0.2.cp.txt.matrix
Research works that cited this repository
- Jisen Zhang, Anupma Sharma, Qingyi Yu, Jianping Wang, Leiting Li, Lin Zhu, Xingtan Zhang, Youqiang Chen, Ray Ming. Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. BMC Genomics, 2016, 17:446. doi:10.1186/s12864-016-2817-9; pmid:27287040
- Jisen Zhang, Qing Zhang, Leiting Li, Haibao Tang, Qiong Zhang, Yang Chen, Jie Arro, Xingtan Zhang, Aiqin Wang, Chenyong Miao, Ray Ming. Recent Polyploidization Events in Three Saccharum Founding Species. Plant Biotechnology Journal, 2018. doi:10.1186/s12864-016-2817-9