bumblenick
commented
6 years ago Alkes Price's lab maintains the perl script but I'll bet that samples.eigen.snp is not in reichlab format. Chromosome values are {1-22, X, Y} and are in the second column. snpnames (like LT635612.1 ??) are in the first column. See examples.
Nick
On Wed, Feb 7, 2018 at 4:10 PM, mike2vandy notifications@github.com wrote:
~/betterSoftware/EIG/bin/smartpca.perl -i samples.eigen.geno -a samples.eigen.snp -b samples.eigen.ind -o test.pca -p test -e test.eigan.eval -l test.log
smartpca -p test.pca.par >test.log fatalx: bad chrom: LT635612.1 sh: line 1: 4589 Aborted (core dumped) smartpca -p test.pca.par > test.log ploteig -i test.pca.evec -c 1:2 -p -x -y -o test.xtxt evec2pca.perl 10 test.pca.evec samples.eigen.ind test.pca
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mike2vandy
~/betterSoftware/EIG/bin/smartpca.perl \ -i samples.eigen.geno \ -a samples.eigen.snp -b samples.eigen.ind \ -o test.pca \ -p test \ -e test.eigan.eval \ -l test.log
smartpca -p test.pca.par >test.log fatalx: bad chrom: LT635612.1 sh: line 1: 4589 Aborted (core dumped) smartpca -p test.pca.par > test.log ploteig -i test.pca.evec -c 1:2 -p -x -y -o test.xtxt evec2pca.perl 10 test.pca.evec samples.eigen.ind test.pca