please explain

[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

[bumblenick]

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 ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#23>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_h0y0cCchCut3CX0dRxP999s9cl38ks5tShEugaJpZM4R9ZVM> .

[mike2vandy]

So if my .snp file looks like:

snp#0 LT635612.1 6e-06 6 G T
snp#1 LT635612.1 7e-05 70 A C
snp#2 LT635612.1 9.2e-05 92 T A
snp#3 LT635612.1 9.3e-05 93 A T
snp#4 LT635612.1 0.000121 121 C T
snp#5 LT635612.1 0.000124 124 T C
snp#6 LT635612.1 0.000125 125 T C
snp#7 LT635612.1 0.000131 131 A T
snp#8 LT635612.1 0.000148 148 G A
snp#9 LT635612.1 0.000159 159 A T

Can eigensoft not recognize chromosome/contigs names != {1-22, X, Y}? Can that be fixed?

[bumblenick]

Nope: Your C-names won't parse. You will have to find a way to change them. N

…

On Fri, Feb 9, 2018 at 1:15 PM, mike2vandy ***@***.***> wrote: So if my .snp file looks like: snp#0 LT635612.1 6e-06 6 G T snp#1 LT635612.1 7e-05 70 A C snp#2 LT635612.1 9.2e-05 92 T A snp#3 LT635612.1 9.3e-05 93 A T snp#4 LT635612.1 0.000121 121 C T snp#5 LT635612.1 0.000124 124 T C snp#6 LT635612.1 0.000125 125 T C snp#7 LT635612.1 0.000131 131 A T snp#8 LT635612.1 0.000148 148 G A snp#9 LT635612.1 0.000159 159 A T Can eigensoft not recognize chromosome/contigs names != {1-22, X, Y}? Can that be fixed? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_h1FrEmHaDTfz_vhv0nAcdS42jy90ks5tTIs4gaJpZM4R9ZVM> .

[mike2vandy]

Imagine if BWA were built this way...

[bumblenick]

Feel free to rewrite the software! Nick

…

On Fri, Feb 9, 2018 at 1:35 PM, mike2vandy ***@***.***> wrote: Imagine if BWA were built this way... — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_h68cSwQ3La6nmEvh3OH3mXU3ICm0ks5tTI_4gaJpZM4R9ZVM> .