Cacher is the code snippet organizer for pro developers

#Load Java
module load java  #requires 1.8
#Install Latest Version of Picard
git clone git@github.com:broadinstitute/picard.git
#Add 'chr' to VCF file if necessary
#awk '{if($0 !~ /^#/) print "chr"$0; else print $0}' all-panctx-merged.vcf > all-panctx-merged_chr.vcf
cd ~/project-geschwind/ASD_pancortical_RNAseq/processed_data/genotyping/mergedvcf/
PICARD=/u/home/g/gandalm/project-geschwind/bin/picard/build/libs/picard.jar
java -Xmx6000m -jar /u/local/apps/picard-tools/2.9.0/picard.jar LiftoverVcf \
  I=all-panctx-merged_chr.vcf \
  O=all-panctx-merged_hg38liftOver.vcf \
  C=/u/project/geschwind/gandalm/RefGenome/Homo_sapiens/hg38/liftOver/hg19ToHg38.over.chain2 \
  REJECT=rejected.vcf \
  R=/u/home/g/gandalm/project-geschwind/RefGenome/Homo_sapiens/hg38/Fasta/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa

FASTA_FILE=/u/nobackup/dhg/Software/Genomes/GRCh37_Gencode25/Homo_sapiens.GRCh37.75.dna.primary_assembly.withERCC.fa                            # reference file used for alignment
GTF_FILE=/u/nobackup/dhg/Software/Genomes/GRCh37_Gencode25/gencode.v25lift37.annotation.noChr.gtf


module load java java/1.8.0_77

export _JAVA_OPTIONS=-Xmx16g
java -Xmx4G -jar ~/bin/QoRTs/QoRTs.jar QC \
                   --generatePlots  \
                   F1R1.merged.bam  \
                   $GTF_FILE  \
                   .