A procedure to call single dose SNP from pileup format
- Author: Lei-Ting Li
- Email: lileiting@gmail.com
- LICENCE: BSD
git clone https://github.com/lileiting/Pileup2singledose.git
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
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