diff --git a/Genome-Reference-File-Retreival/All.chrs.GRCh38.genotypes.20170504.bcf.sh b/Genome-Reference-File-Retreival/All.chrs.GRCh38.genotypes.20170504.bcf.sh
deleted file mode 100644
index 7d396d1..0000000
--- a/Genome-Reference-File-Retreival/All.chrs.GRCh38.genotypes.20170504.bcf.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!bin/bash
-
-####################################################                                               
-# Set env variables and  work directory                                                            ####################################################                                                                                                            
-export REFDIR="/media/drew/easystore/ReferenceGenomes"
-export IDXDIR=$REFDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set/
-export REFFA=$IDXDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
-cd $IDXDIR
-
-#wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/ALL.chr{{1..22},X,Y}_GRCh38.genotypes.20170504.vcf.gz{,.tbi}
-
-#for chr in {1..22} X Y; do
-for chr in X Y; do
-  (bcftools view --no-version -h ALL.chr${chr}_GRCh38.genotypes.20170504.vcf.gz | \
-    grep -v "^##contig=<ID=[GNh]" | sed 's/^##contig=<ID=MT/##contig=<ID=chrM/;s/^##contig=<ID=\([0-9XY]\)/##contig=<ID=chr\1/'; \
-  bcftools annotate --no-version -x INFO/END ALL.chr${chr}_GRCh38.genotypes.20170504.vcf.gz | \
-  bcftools view --no-version -H -c 2 | \
-  grep -v "[0-9]|\.\|\.|[0-9]" | sed 's/^/chr/') | \
-  bcftools norm --no-version -Ou -m -any | \
-  bcftools norm --no-version -Ob -o ALL.chr${chr}_GRCh38.genotypes.20170504.bcf \
-	   -d none -f $REFFA && bcftools index -f ALL.chr${chr}_GRCh38.genotypes.20170504.bcf
-done
diff --git a/Genome-Reference-File-Retreival/CreateMaptsv.sh b/Genome-Reference-File-Retreival/CreateMaptsv.sh
deleted file mode 100644
index 9091e89..0000000
--- a/Genome-Reference-File-Retreival/CreateMaptsv.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!bin/bash
-workdir="~/Downloads/GoodCell-Resources/GuniosAnalysis/"
-for file in  $workdir/ReferenceGenomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set/;do
-    ln -s $file
-done
-for file in ~/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GSA_24v1_0/;do
-    ln -s $file
-done
-ln -s $HOME/res/ensembl/Homo_sapiens.GRCh38.fixed.98.gff3.gz
-#ln -s $workdir/ReferenceGenomes/clinvar/clinvar_$date.GRCh38.vcf.gz
-#ln -s $workdir/ReferenceGenomes/clinvar/clinvar_$date.GRCh38.vcf.gz.tbi
-declare -A dirs=( ["20180117"]="2018_07" ["20200110"]="2020_01" )
-declare	-A bpms=( ["20180117"]="~/Downloads/GoodCell-Resources/GuniosAnalysis/2018_07/GenomeStudio_Files/Manifest_Files/GSA-24v1-0_A2.bpm" ["20200110"]="~/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GSA_24v2_0/GSA-24v2-0_A2.bpm" )
-declare -A egts=( ["20180117"]="~/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GSA_24v1_0/GSA-24v1-0_A2_ClusterFile.egt" ["20200110"]="~/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GSA_24v2_0/GSA-24v2-0_A2_ClusterFile.egt" )
-declare	-A csv=( ["20180117"]="~/Downloads/GoodCell-Resources/GuniosAnalysis/2018_07/GenomeStudio_Files/Manifest_Files/GSA-24v1-0_A2.csv" ["20200110"]="~/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GSA_24v2_0/GSA-24v2-0_A2.csv" )
-##########################################################################
-## CONVERT GSA DATA FROM IDAT TO GTC                                     ##
-###########################################################################
-workdir=" ~/Downloads/GoodCell-Resources/GuniosAnalysis/2018_07/"
-cd $workdir
-export BCFTOOLS_PLUGINS=$HOME/bin/bcftools/plugins
-for pfx in $(dirs); do
-    bpm="./GenomeStudio_Files/Manifest_Files/GSA-24v1-0_A1.bpm"
-    egt="$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GSA_24v1_0/GSA-24v1-0_A1_ClusterFile.egt"
-    csv="$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GSA_24v1_0/GSA-24v1-0_A1.csv"
-    echo $egt
-    echo $csv
-    echo $bpm
-    bcftools +gtc2vcf --gtcs  GTCs -o maps.tsv
-    #/bin/rm *.idat
-done
diff --git a/Genome-Reference-File-Retreival/GRCh37_Reference_Genome_Retreival.sh b/Genome-Reference-File-Retreival/GRCh37_Reference_Genome_Retreival.sh
deleted file mode 100644
index 230d869..0000000
--- a/Genome-Reference-File-Retreival/GRCh37_Reference_Genome_Retreival.sh
+++ /dev/null
@@ -1,54 +0,0 @@
-#!bin/bash
-# Reference Genome Retreival Script
-export REFDIR="/media/drew/easystore/ReferenceGenomes/GRCh37"
-cd $REFDIR
-# GRCh37
-wget -O- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz | gzip -d > human_g1k_v37.fasta
-samtools faidx human_g1k_v37.fasta
-
-# Genetic map
-wget https://data.broadinstitute.org/alkesgroup/Eagle/downloads/tables/genetic_map_hg19_withX.txt.gz
-
-# 1000 Genomes project phase 3
-for chr in {1..22} X Y; do
-    bcftools view --no-version -Ou -c 2 ALL.chr${chr}.phase3*integrated_v[125][ab].20130502.genotypes.vcf.gz | \
-	bcftools norm --no-version -Ou -m -any | \
-	bcftools norm --no-version -Ob -o ALL.chr${chr}.phase3_integrated.20130502.genotypes.bcf -d none -f human_g1k_v37.fasta && \
-	bcftools index -f ALL.chr${chr}.phase3_integrated.20130502.genotypes.bcf
-done
-
-# List of common germline duplications and deletions
-wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz{,.tbi}
-bcftools query -i 'AC>1 && END-POS+1>10000 && SVTYPE!="INDEL" && (SVTYPE=="CNV" || SVTYPE=="DEL" || SVTYPE=="DUP")' \
-	 -f "%CHROM\t%POS0\t%END\t%SVTYPE\n" ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz > cnp.grch37.bed
-
-# Minimal divergence intervals from segmental duplications
-wget -O- http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/genomicSuperDups.txt.gz | gzip -d |
-  awk '!($2=="chrX" && $8=="chrY" || $2=="chrY" && $8=="chrX") {print $2"\t"$3"\t"$4"\t"$30}' > genomicSuperDups.bed
-
-awk '{print $1,$2; print $1,$3}' genomicSuperDups.bed | \
-  sort -k1,1 -k2,2n | uniq | \
-  awk 'chrom==$1 {print chrom"\t"pos"\t"$2} {chrom=$1; pos=$2}' | \
-  bedtools intersect -a genomicSuperDups.bed -b - | \
-  bedtools sort | \
-  bedtools groupby -c 4 -o min | \
-  awk 'BEGIN {i=0; s[0]="+"; s[1]="-"} {if ($4!=x) i=(i+1)%2; x=$4; print $0"\t0\t"s[i]}' | \
-  bedtools merge -s -c 4 -o distinct | \
-  sed 's/^chr//' | grep -v gl | bgzip > dup.grch37.bed.gz && \
-  tabix -f -p bed dup.grch37.bed.gz
-
-# Download cytoband file
-wget -O cytoBand.hg19.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz
-
-
-# Setup variables
-ref="$REFDIR/human_g1k_v37.fasta"
-mhc_reg="6:27486711-33448264"
-kir_reg="19:54574747-55504099"
-map="$REFDIR/genetic_map_hg19_withX.txt.gz"
-kgp_pfx="$REFDIR/ALL.chr"
-kgp_sfx=".phase3_integrated.20130502.genotypes"
-rule="GRCh37"
-cnp="$REFDIR/cnp.grch37.bed"
-dup="$REFDIR/dup.grch37.bed.gz"
-cyto="$REFDIR/cytoBand.hg19.txt.gz"
diff --git a/MiSeqScripts/1.MiSeq-index-and-bwa-mem.sh b/MiSeqScripts/1.MiSeq-index-and-bwa-mem.sh
index d7b2144..5e418e4 100644
--- a/MiSeqScripts/1.MiSeq-index-and-bwa-mem.sh
+++ b/MiSeqScripts/1.MiSeq-index-and-bwa-mem.sh
@@ -24,12 +24,12 @@ for pfx in 2019_09 2019_12; do
     datadir=${datadir[$pfx]}
     cd $miseqdir
     export WORK_DIR=./$datadir
-    mkdir -p ./MiSeq_Results_out
+    mkdir -p ./MiSeq_Results_out/1.RAW_BAMS
     touch ./sm.file.txt
     touch ./sm.txt
     export INPUT_FILE=./sm.file.txt
     export INPUTFILE=./sm.txt
-    export RESULTS=MiSeq_Results_out
+    export RESULTS=/MiSeq_Results_out/1.RAW_BAMS
     find -iname "*_R1_*.fastq.gz" > $INPUT_FILE
     for i in $(cat $INPUT_FILE); do
 	basename -s "R1_001.fastq.gz" $i >> $INPUTFILE
diff --git a/MiSeqScripts/2.MiSeq-remove_dups.sh b/MiSeqScripts/2.MiSeq-remove_dups.sh
index b797f8e..fc50d4a 100644
--- a/MiSeqScripts/2.MiSeq-remove_dups.sh
+++ b/MiSeqScripts/2.MiSeq-remove_dups.sh
@@ -26,13 +26,16 @@ for pfx in 2019_09 2019_12; do
     export WORKDIR=$WORK_DIR/$miseqdir
     export INPUT_FILE=$WORKDIR/sm.txt
     cd $WORKDIR
+    mkdir -p $datadir/2.TMP_DUP_BAMS
+    export INPUT=$datadir/1.RAW_BAMS
+    export OUTPUT=$datadir/2.TMP_DUP_BAMS
     sm_arr=( $(cat $INPUT_FILE) )
     n=${#sm_arr[@]}
     for i in $(seq 1 $n); do
 	sm_arr=( $(cat $INPUT_FILE) ); \
 	sm=${sm_arr[(($i-1))]}; \
-	java -jar $HOME/toolbin/picard.jar MarkDuplicates I=$datadir/$sm.raw.bam  \
-	    O=$datadir/$sm.tmp.bam M=$datadir/$sm.dups_metrics.txt && \
-	    samtools index $datadir/$sm.tmp.bam
+	java -jar $HOME/toolbin/picard.jar MarkDuplicates I=$INPUT/$sm.raw.bam  \
+	    O=$OUTPUT/$sm.tmp.bam M=$OUTPUT/$sm.dups_metrics.txt && \
+	    samtools index $OUTPUT/$sm.tmp.bam
     done
 done
diff --git a/MiSeqScripts/3.MiSeq-recalibrate_basepairs.sh b/MiSeqScripts/3.MiSeq-recalibrate_basepairs.sh
index 1c41a03..3a71bbb 100644
--- a/MiSeqScripts/3.MiSeq-recalibrate_basepairs.sh
+++ b/MiSeqScripts/3.MiSeq-recalibrate_basepairs.sh
@@ -12,29 +12,27 @@ export REFFA=$IDXDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
 export VCF1000G=$REFDIR/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz
 export TBI1000G=$REFDIR/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi
 
-for file in $IDXDIR; do
-    ln -s $file
-done
-
 declare -A miseqdir=( ["2019_09"]="2019_09" ["2019_12"]="2019_12" )
 declare -A datadir=( ["2019_09"]="MiSeq_Results_out" ["2019_12"]="MiSeq_Results_out" )
 
 for pfx in 2019_09 2019_12; do
     miseqdir=${miseqdir[$pfx]}
     datadir=${datadir[$pfx]}
-    export WORK_DIR=$WORKDIR/$miseqdir
-    export INPUT_FILE=$WORK_DIR/sm.txt
-    cd $WORK_DIR
+    cd $miseqdir
+    mkdir -p $datadir/3.GRP_BAMs
+    export OUTDIR=$datadir/3.GRP_BAMs
+    export INPUT_FILE=sm.txt
+    export INPUTDIR=$datadir/2.TMP_DUP_BAMs
     sm_arr=( $(cat $INPUT_FILE) )
     n=${#sm_arr[@]}
     for i in $(seq 1 $n); do
 	sm_arr=( $(cat $INPUT_FILE) );
 	sm=${sm_arr[(($i-1))]};
-	$GATK BaseRecalibrator -R $REFFA -I $datadir/$sm.tmp.bam --known-sites $VCF1000G \
-	      -O $datadir/$sm.grp && \
-	$GATK ApplyBQSR -R $REFFA -I $datadir/$sm.tmp.bam \
-	      --bqsr-recal-file $datadir/$sm.grp -O $datadir/$sm.bam && \
-	    samtools index $datadir/$sm.bam
+	$GATK BaseRecalibrator -R $REFFA -I $INPUTDIR/$sm.tmp.bam --known-sites $VCF1000G \
+	      -O $OUTDIR/$sm.grp && \
+	$GATK ApplyBQSR -R $REFFA -I $INPUTDIR/$sm.tmp.bam \
+	      --bqsr-recal-file $OUTDIR/$sm.grp -O $OUTDIR/$sm.bam && \
+	    samtools index $OUTDIR/$sm.bam
     done
 done
 
diff --git a/MiSeqScripts/4.MiSeq-coverage.sh b/MiSeqScripts/4.MiSeq-coverage.sh
index 24118ba..96869da 100644
--- a/MiSeqScripts/4.MiSeq-coverage.sh
+++ b/MiSeqScripts/4.MiSeq-coverage.sh
@@ -1,35 +1,47 @@
 #!bin/bash
 
 ###########################################################################
-# MISEQ DATA                                                            
-# PILOT DATA                                                           
+# Export Env Variables
 ###########################################################################
 
+export GATK=$HOME/toolbin/gatk-4.1.8.1/gatk
 export REFDIR=/media/drew/easystore/ReferenceGenomes/
-export BEDDIR=/media/drew/easystore/ReferenceGenomes/BEDs
+export BEDDIR=$REFDIR/BEDs
 export BEDFILE=$BEDDIR/3215481_Covered.bed
-export IDXDIR=$REFDIR/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set
-export REFFILE=$IDXDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
-export REFFAI=$IDXDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai
-
-for file in $IDXDIR; do
-    ln -s $file
-done
-
-#cd ~/Downloads/GoodCell-Resources/GuniosAnalysis/2019_09/LVB_fastq_Sept2019_concat_fastq
-#find -iname "*_R1_0012.fastq.gz" | cut -d/ -f2 | cut -d_ -f1 >> ../sm.txt
 
+export IDXDIR=$REFDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set
+export REFFA=$IDXDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
+export REFFAI=$IDXDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai
+export WORKDIR=/media/drew/easystore/GoodCell-Resources/AnalysisBaseDir/MiSeq_Data
 ###########################################################################
 ## COMPUTE COVERAGE OVER TARGETS                                         ##
 ###########################################################################
 
-sm_arr=( $(cat sm.txt) )
-n=${#sm_arr[@]}
-for sm in ${sm_arr[@]}; do
-  bedtools coverage -g $REFFAI -sorted -a $BEDFILE -b $sm.bam -mean | \
-  cut -f5 > $sm.cov
+declare -A miseqdir=( ["2019_09"]="2019_09" ["2019_12"]="2019_12" )
+declare -A datadir=( ["2019_09"]="MiSeq_Results_out/3.GRP_BAMs" ["2019_12"]="MiSeq_Results_out/3.GRP_BAMs" )
+declare -A coverage=( ["2019_09"]="MiSeq_Results_out/Coverage_out" ["2019_12"]="MiSeq_Results_out/Coverage_out" )
+declare -A v2s=( ["2019_09"]="MiSeq_Results_out/4.V2_BAMs" ["2019_12"]="MiSeq_Results_out/4.V2_BAMs" )
+
+for pfx in 2019_09 2019_12; do
+    miseqdir=${miseqdir[$pfx]}
+    datadir=${datadir[$pfx]}
+    coverage=${coverage[$pfx]}
+    cd $WORKDIR/$miseqdir
+    export INPUT_FILE=sm.txt
+    export INPUTDIR=$datadir
+    export OUTPUT=$coverage
+    sm_arr=( $(cat $INPUT_FILE) )
+    n=${#sm_arr[@]}
+    echo $n
+    for i in $(seq 1 $n); do
+	sm_arr=( $(cat $INPUT_FILE) );
+	sm=${sm_arr[(($i-1))]};
+	echo $sm
+	pwd
+	bedtools coverage -g $REFFAI -sorted -a $BEDFILE -b $INPUTDIR/$sm.bam -mean | \
+	    cut -f5 >  $OUTPUT/$sm.cov
+    done
+    (echo -en "CHROM\tBEG\tEND\tNAME\t"; tr '\n' '\t' < sm.txt | sed 's/\t$/\n/'; \
+     paste $BEDFILE $(cat sm.txt | sed 's/$/.cov/' | tr '\n' '\t' | sed 's/\t$/\n/')) \
+	>  $BEDDIR/3215481_Covered.GRCh38.tsv
 done
-(echo -en "CHROM\tBEG\tEND\tNAME\t"; tr '\n' '\t' < sm.txt | sed 's/\t$/\n/'; \
- paste $BEDFILE $(cat sm.txt | sed 's/$/.cov/' | tr '\n' '\t' | sed 's/\t$/\n/')) \
-    > 3215481_Covered.GRCh38.tsv
-#/bin/rm $(cat sm.txt | sed 's/$/.cov/' | tr '\n' '\t' | sed 's/\t$/\n/')
diff --git a/MiSeqScripts/4.MiSeq-coverage.sh.~1~ b/MiSeqScripts/4.MiSeq-coverage.sh.~1~
new file mode 100644
index 0000000..505b64a
--- /dev/null
+++ b/MiSeqScripts/4.MiSeq-coverage.sh.~1~
@@ -0,0 +1,44 @@
+#!bin/bash
+
+###########################################################################
+# Export Env Variables
+###########################################################################
+
+export GATK=$HOME/toolbin/gatk-4.1.8.1/gatk
+export REFDIR=/media/drew/easystore/ReferenceGenomes/
+export BEDDIR=$REFDIR/BEDs
+export BEDFILE=$BEDDIR/3215481_Covered.bed
+
+export IDXDIR=$REFDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set
+export REFFA=$IDXDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
+export REFFAI=$IDXDIR/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai
+export WORKDIR=/media/drew/easystore/GoodCell-Resources/AnalysisBaseDir/MiSeq_Data
+###########################################################################
+## COMPUTE COVERAGE OVER TARGETS                                         ##
+###########################################################################
+
+declare -A miseqdir=( ["2019_09"]="2019_09" ["2019_12"]="2019_12" )
+declare -A datadir=( ["2019_09"]="MiSeq_Results_out/3.GRP_BAMs" ["2019_12"]="MiSeq_Results_out/3.GRP_BAMs" )
+declare -A coverage=( ["2019_09"]="MiSeq_Results_out/Coverage_out" ["2019_12"]="MiSeq_Results_out/Coverage_out" )
+declare -A v2s=( ["2019_09"]="MiSeq_Results_out/4.V2_BAMs" ["2019_12"]="MiSeq_Results_out/4.V2_BAMs" )
+
+for pfx in 2019_09 2019_12; do
+    miseqdir=${miseqdir[$pfx]}
+    datadir=${datadir[$pfx]}
+    coverage=${coverage[$pfx]}
+    cd $WORKDIR/$miseqdir
+    export INPUT_FILE=sm.txt
+    export INPUTDIR=$datadir
+    export OUTPUT=$coverage
+    sm_arr=( $(cat $INPUT_FILE) )
+    n=${#sm_arr[@]}
+    for i in $(seq 1 $n); do
+	sm_arr=( $(cat $INPUT_FILE) );
+	sm=${sm_arr[(($i-1))]};
+	bedtools coverage -g $REFFAI -sorted -a $BEDFILE -b $INPUTDIR/$sm.bam -mean | \
+	    cut -f5 >  $OUTPUT/$sm.cov
+    done
+    (echo -en "CHROM\tBEG\tEND\tNAME\t"; tr '\n' '\t' < sm.txt | sed 's/\t$/\n/'; \
+     paste $BEDFILE $(cat sm.txt | sed 's/$/.cov/' | tr '\n' '\t' | sed 's/\t$/\n/')) \
+	>  $BEDDIR/3215481_Covered.GRCh38.tsv
+done
diff --git a/MiSeqScripts/4.MiSeq-coverage.sh~ b/MiSeqScripts/4.MiSeq-coverage.sh~
deleted file mode 100644
index a3389f8..0000000
--- a/MiSeqScripts/4.MiSeq-coverage.sh~
+++ /dev/null
@@ -1,41 +0,0 @@
-#!bin/bash
-
-###########################################################################
-# MISEQ DATA                                                            
-# PILOT DATA                                                           
-###########################################################################
-
-export REFDIR=$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/
-
-export IDX_DIR=$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set
-
-export REF_FILE=$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
-
-for file in $IDX_DIR; do
-    ln -s $file
-done
-
-cd ~/Downloads/GoodCell-Resources/GuniosAnalysis/2019_09/LVB_fastq_Sept2019_concat_fastq
-find -iname "*_R1_0012.fastq.gz" | cut -d/ -f2 | cut -d_ -f1 >> ../sm.txt
-
-mkdir -P ../MiSeqResults/raw-sams
-mkdir -P ../MiSeqResults/raw-bams
-mkdir -P ../MiSeqResults/tmp-bams
-mkdir -P ../MiSeqResults/idx-bams
-
-###########################################################################
-## COMPUTE COVERAGE OVER TARGETS                                         ##
-###########################################################################
-
-ln -s $HOME/res/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai
-
-sm_arr=( $(cat sm.txt) )
-n=${#sm_arr[@]}
-for sm in ${sm_arr[@]}; do
-  bedtools coverage -g GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai -sorted -a 3215481_Covered.GRCh38.bed -b $sm.bam -mean | \
-  cut -f5 > $sm.cov
-done
-(echo -en "CHROM\tBEG\tEND\tNAME\t"; tr '\n' '\t' < sm.txt | sed 's/\t$/\n/'; \
-paste 3215481_Covered.GRCh38.bed $(cat sm.txt | sed 's/$/.cov/' | tr '\n' '\t' | sed 's/\t$/\n/')) \
-  > 3215481_Covered.GRCh38.tsv
-/bin/rm $(cat sm.txt | sed 's/$/.cov/' | tr '\n' '\t' | sed 's/\t$/\n/')
diff --git a/MiSeqScripts/Lift-over-Targets.sh~ b/MiSeqScripts/Lift-over-Targets.sh~
deleted file mode 100644
index c04a1ef..0000000
--- a/MiSeqScripts/Lift-over-Targets.sh~
+++ /dev/null
@@ -1,8 +0,0 @@
-#!bin/bash
-export REFDIR=/media/drew/easystore/ReferenceGenomes
-export BEDDIR=/media/drew/easystore/ReferenceGenomes/BEDs
-export BEDFILE=$BEDDIR/3215481_Covered.bed
-export LIFTOVER=$REFDIR/GRCh38/hg19ToHg38.over.chain.gz
-
-grep ^chr $BEDFILE | liftOver  /dev/stdin $LIFTOVER hg19ToHg38.over.chain.gz \
-			       $BEDFILE  /dev/stderr
diff --git a/MiSeqScripts/MiSeq-fastq-alignment.sh b/MiSeqScripts/MiSeq-fastq-alignment.sh
deleted file mode 100644
index 4cb798a..0000000
--- a/MiSeqScripts/MiSeq-fastq-alignment.sh
+++ /dev/null
@@ -1,76 +0,0 @@
-#!bin/bash
-
-###########################################################################
-# MISEQ DATA                                                            
-# PILOT DATA                                                           
-###########################################################################
-
-export REFDIR=$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/
-
-export IDX_DIR=$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set
-
-export REF_FILE=$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
-
-for file in $IDX_DIR; do
-    ln -s $file
-done
-
-cd ~/Downloads/GoodCell-Resources/GuniosAnalysis/2019_09/LVB_fastq_Sept2019_concat_fastq
-find -iname "*_R1_0012.fastq.gz" | cut -d/ -f2 | cut -d_ -f1 >> ../sm.txt
-
-mkdir -P ../MiSeqResults/raw-sams
-mkdir -P ../MiSeqResults/raw-bams
-mkdir -P ../MiSeqResults/tmp-bams
-mkdir -P ../MiSeqResults/idx-bams
-
-#for sfx in 1-1 1-2 1-3 2-1 2-2 2-3 2-4 3-1 3-2 3-3; do
-#  unzip raw/Batch$sfx.zip
-#done
-
-#find -iname "*_R1_0[01][12].fastq.gz" | grep -v "MPC10\|NA12878\|NA18507" | cut -d/ -f4 | cut -d_ -f1 >> sm.txt
-
-## NEXTSEQ DATA                                                         
-#unzip FASTQ_Part1.zip
-#unzip FASTQ_Part2.zip
-#find -iname "*_R1_001.fastq.gz" | cut -d/ -f2 | cut -d_ -f1 >> sm.txt
-
-###########################################################################
-## FASTQ ALIGNMENT                                                       ##
-###########################################################################
-
-sm_arr=( $(cat ../sm.txt) )
-n=${#sm_arr[@]}
-
-# pilot data and MiSeq data
-for i in $(seq 1 $n); do
-  fastq_arr=( $(find -iname "*_R1_0012.fastq.gz" | grep -v "MPC10\|NA12878\|NA18507") ); \
-  sm_arr=( $(cat ../sm.txt) ); \
-  fastq_r1=${fastq_arr[(($i-1))]}; \
-  fastq_r2=${fastq_r1%_R1_0012.fastq.gz}_R2_0012.fastq.gz; \
-  sm=${sm_arr[(($i-1))]}; \
-  str="@RG\tID:$sm\tPL:ILLUMINA\tPU:$sm\tLB:$sm\tSM:$sm"; \
-  bwa mem -M -R "$str" $IDX_DIR $fastq_r1 $fastq_r2 -o ../MiSeqResults/raw-sam/$sm.raw.sam
-  samtools view -Sb -o  ../MiSeqResults/raw-bam/$sm.raw.bam
-  samtools sort -T $sm -O BAM -o ../MiSeqResults/tmp-bam/$sm.tmp.bam ../MiSeqResults/raw-bam/$sm.raw.bam
-  samtools index -b -@ 2 ../MiSeqResults/raw-bam/$sm.raw.bam ../MiSeqResults/idx-bam/$sm.idx.bam
-done
-
-###########################################################################
-## REMOVE DUPLICATES                                                     ##
-###########################################################################
-
-ln -s $HOME/bin/picard.jar
-
-sm_arr=( $(cat ../sm.txt) )
-n=${#sm_arr[@]}
-for i in $(seq 1 $n); do
-  sm_arr=( $(cat ../sm.txt) ); \
-  sm=${sm_arr[(($i-1))]}; \
-  java \
-    -jar picard.jar \
-    MarkDuplicates \
-    I=$sm.raw.bam \
-    O=$sm.tmp.bam \
-    M=$sm.txt && \
-  samtools index $sm.tmp.bam
-done
diff --git a/MiSeqScripts/MiSeq-recalibrate.sh b/MiSeqScripts/MiSeq-recalibrate.sh
deleted file mode 100644
index 14895dd..0000000
--- a/MiSeqScripts/MiSeq-recalibrate.sh
+++ /dev/null
@@ -1,52 +0,0 @@
-#!bin/bash
-
-###########################################################################
-# MISEQ DATA                                                            
-# PILOT DATA                                                           
-###########################################################################
-
-export REFDIR=$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/
-
-export IDX_DIR=$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set
-
-export REF_FILE=$HOME/Downloads/GoodCell-Resources/GuniosAnalysis/ReferenceGenomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
-
-for file in $IDX_DIR; do
-    ln -s $file
-done
-
-cd ~/Downloads/GoodCell-Resources/GuniosAnalysis/2019_09/LVB_fastq_Sept2019_concat_fastq
-find -iname "*_R1_0012.fastq.gz" | cut -d/ -f2 | cut -d_ -f1 >> ../sm.txt
-
-mkdir -P ../MiSeqResults/raw-sams
-mkdir -P ../MiSeqResults/raw-bams
-mkdir -P ../MiSeqResults/tmp-bams
-mkdir -P ../MiSeqResults/idx-bams
-###########################################################################
-## RECALIBRATE BASE PAIRS                                                ##
-###########################################################################
-
-ln -s $HOME/bin/gatk-4.1.3.0
-ln -s $HOME/Downloads/GCA_000001405.15_GRCh38_no_alt_analysis_set.dict
-ln -s $HOME/res/vqsr/1000G_phase1.snps.high_confidence.hg38.vcf.gz
-ln -s $HOME/res/vqsr/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi
-
-sm_arr=( $(cat sm.txt) )
-n=${#sm_arr[@]}
-for i in $(seq 1 $n); do
-  sm_arr=( $(cat sm.txt) ); \
-  sm=${sm_arr[(($i-1))]}; \
-  gatk-4.1.3.0/gatk \
-    BaseRecalibrator \
-    -R GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
-    -I $sm.tmp.bam \
-    --known-sites 1000G_phase1.snps.high_confidence.hg38.vcf.gz \
-    -O $sm.grp && \
-  gatk-4.1.3.0/gatk \
-    ApplyBQSR \
-    -R GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
-    -I $sm.tmp.bam \
-    --bqsr-recal-file $sm.grp \
-    -O $sm.bam && \
-  samtools index $sm.bam
-done
diff --git a/misc/#CreateMaptsv.new.sh# b/misc/#CreateMaptsv.new.sh#
new file mode 100644
index 0000000..78e6203
--- /dev/null
+++ b/misc/#CreateMaptsv.new.sh#
@@ -0,0 +1,39 @@
+#!bin/bash
+
+##############################################################################
+# Set env variables and create array of microarrya data directories
+##############################################################################
+
+export WORKDIR="/media/drew/easystore/AnalysisBaseDir/GSA_Data"
+declare -A wdir=( ["20180117"]="2018_07" ["20200110"]="2020_01" )
+
+##############################################################################
+# create input file with the IDAT fles and from those create maps
+##############################################################################
+
+for pfx in 20180117 20200110; do
+    wdir=${wdir[$pfx]}
+    touch $WORKDIR/$wdir/dir.txt
+    cd $WORKDIR/$wdir
+    find -iname "*_idat" | xargs ./dir.txt
+    for f in ./dir.txt; do
+	dir=$f
+	cd $dir
+	find -iname "*.idat" | xargs > $WORKDIR/$wdir/files.txt
+done
+
+    bcftools +gtc2vcf --gtcs  GTCs -o $wdir.maps.tsv
+
+
+for f in $WORKDIR/$wdir/files.txt; do
+    bcftools +gtc2vcf -i -g $f
+done
+
+done
+	  
+	  
+	  
+	  
+	  
+	  
+
diff --git a/misc/.#CreateMaptsv.new.sh b/misc/.#CreateMaptsv.new.sh
new file mode 120000
index 0000000..0115f3e
--- /dev/null
+++ b/misc/.#CreateMaptsv.new.sh
@@ -0,0 +1 @@
+drew@drew-hp-pavilion.114235:1603135760
\ No newline at end of file
diff --git a/MiSeqScripts/0.make-index-files b/misc/0.make-index-files
similarity index 100%
rename from MiSeqScripts/0.make-index-files
rename to misc/0.make-index-files
diff --git a/Genome-Reference-File-Retreival/1000genomes-GRCh38-and-others.sh b/misc/1000genomes-GRCh38-wget.sh
similarity index 100%
rename from Genome-Reference-File-Retreival/1000genomes-GRCh38-and-others.sh
rename to misc/1000genomes-GRCh38-wget.sh
diff --git a/misc/CreateMaptsv.new.sh b/misc/CreateMaptsv.new.sh
new file mode 100644
index 0000000..c7d105d
--- /dev/null
+++ b/misc/CreateMaptsv.new.sh
@@ -0,0 +1,54 @@
+#!bin/bash
+
+##############################################################################
+# Set env variables
+##############################################################################
+
+export date="20200810"
+export wrkdr="/media/drew/easystore/AnalysisBaseDir/GSA_Data"
+export REFDIR="/media/drew/easystore/ReferenceGenomes"
+export REFGFF=$REFDIR/Ensembl/Homo_sapiens.GRCh38.fixed.101.gff3.gz
+export REFVCF=$REFDIR/GRCh38/clinvar_$date.GRCh38.vcf.gz
+export REFTBI=$REFDIR/GRCh38/clinvar_$date.GRCh38.vcf.gz.tbi
+
+##############################################################################
+# create arrays
+##############################################################################
+
+declare -A wdir=( ["20180117"]="2018_07" ["20200110"]="2020_01" )
+declare	-A bpms=( ["20180117"]="/media/drew/easystore/GoodCell-Resources/AnalysisBaseDir/2018_07/GenomeStudio_Files/Manifest_Files/GSA-24v1-0_A2.bpm" ["20200110"]="/media/drew/easystore/ReferenceGenomes/GSA_24v2_0/GSA-24v2-0_A2.bpm" )
+declare -A egts=( ["20180117"]="/media/drew/easystore/ReferenceGenomes/GSA_24v1_0/GSA-24v1-0_A2_ClusterFile.egt" ["20200110"]="/media/drew/easystore/ReferenceGenomes/GSA_24v2_0/GSA-24v2-0_A2_ClusterFile.egt" )
+declare	-A csvs=( ["20180117"]="/media/drew/easystore/GoodCell-Resources/AnalysisBaseDir/2018_07/GenomeStudio_Files/Manifest_Files/GSA-24v1-0_A2.csv" ["20200110"]="/media/drew/easystore/ReferenceGenomes/GSA_24v2_0/GSA-24v2-0_A2.csv" )
+
+##############################################################################
+# iterate over data
+##############################################################################
+
+find -iname "*_idat" | xargs $wrkdr/$wdir/dir.txt
+for f in $wrkdr/$wdir/dir.txt; do
+    dir=$f
+    cd $dir
+    touch $wrkdr/$wdir/files.txt
+    find -iname "*.idat" | xargs > $wrkdr/$wdir/files.txt
+done
+
+for f in $wrkdr/$wdir/files.txt; do
+    bcftools +gtc2vcf -i -g $f
+done
+
+for pfx in 20180117 20200110; do
+    wdir=${wdir[$pfx]}
+    bpm=${bpms[$pfx]}
+    egt=${egts[$pfx]}
+    csv=${csvs[${pfx]}
+    touch $wrkdr/$wdir/dir.txt
+    cd $wrkdr/$wdir
+    bcftools +gtc2vcf --gtcs  GTCs -o $wdir.maps.tsv
+done
+	  
+	  
+	  
+	  
+	  
+	  
+
diff --git a/Genome-Reference-File-Retreival/make_sm.txt.sh b/misc/make_sm.txt.sh
similarity index 100%
rename from Genome-Reference-File-Retreival/make_sm.txt.sh
rename to misc/make_sm.txt.sh