Main README.md was modified to contain the changes in the repository.

Created directories to classify all the scripts and added several files. All are described in the README.md for each directory

New and moved files into DNAseq/
new file:   DNAseq/README.md
new file:   DNAseq/annotate.vcf.sh
new file:   DNAseq/cond.sub.awk
new file:   DNAseq/get_vc.sh
new file:   DNAseq/.keep
renamed:    bwa.map.slq -> DNAseq/bwa.map.slq
renamed:    freeb.vc.slq -> DNAseq/freeb.vc.slq
renamed:    gatk.pp.slq -> DNAseq/gatk.pp.slq
renamed:    gatk.qpp.scala -> DNAseq/gatk.qpp.scala
renamed:    gatk.qpp.sh -> DNAseq/gatk.qpp.sh
renamed:    gatk.qvcf.scala -> DNAseq/gatk.qvc.scala
renamed:    gatk.qvcf.sh -> DNAseq/gatk.qvc.sh
renamed:    plat.vc.slq -> DNAseq/plat.vc.slq
renamed:    q.hc.scala -> DNAseq/q.hc.scala
renamed:    q.hc.sh -> DNAseq/q.hc.sh
renamed:    q.indel.scala -> DNAseq/q.indel.scala
renamed:    q.indel.sh -> DNAseq/q.indel.sh
renamed:    q.submit.sh -> DNAseq/q.submit.sh

New and moved files into RNAseq/
new file:   RNAseq/README.md : contains i
new file:   RNAseq/.keep
renamed:    cuff.analysis.slq -> RNAseq/cuff.analysis.slq
renamed:    idx_htseq.slq -> RNAseq/idx_htseq.slq
renamed:    make.sjdb.sh -> RNAseq/make.sjdb.sh
renamed:    star.2pass.genome.slq -> RNAseq/star.2pass.genome.slq
renamed:    star.2pass.slq -> RNAseq/star.2pass.slq
renamed:    star.cuffX.slq -> RNAseq/star.cuffX.slq
renamed:    star.htseq.slq -> RNAseq/star.htseq.slq
renamed:    star.map.slq -> RNAseq/star.map.slq
renamed:    tophat.map.slq -> RNAseq/tophat.map.slq

Moved files into QTLMapping/
new file:   QTLMapping/.keep
renamed:    geno.image2.R -> QTLMapping/geno.image2.R

new file:   GeneExpression/.keep

deleted:    script.py
Merge branch 'master' of https://github.com/RodrigoGM/mouseomics
?