R Notebook

First remove “#” from headers. Then combine the knownEM_pK-EM. Then read in.

polar<-read.table("~/Desktop/polar_bear.pooled.snp.txt",header=T)

So we need columns from here

rs#    alleles    chrom     pos     strand    assembly#    center    protLSID    assayLSID    panelLSID    QCcode    sample1 etc.

So invent rs# maybe using chrom_position. Then alleles is just major/minor. Then strand “+”. Then assembly, center, prot, assay, panel, QCcode can all be “NA”.

Tassel is on cluster:

[ 10:44AM ]  [ jri@farm:~ ]
$ module load jdk
Module JAVA 1.8.0.31 Loaded.
[ 10:44AM ]  [ jri@farm:~ ]
$ module load tassel
Module tassel/5.2.14 loaded

And so is plink:

[ 10:45AM ]  [ jri@farm:~ ]
$ module load plink/1.90
Module plink/1.90 loaded