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Treemix/imput_data_prep_withassulta.sh

+#!/bin/bash
+#SBATCH -p dgimi-eha
+#SBATCH --mem=50G
+
+module load cv-standard
+module load python/2.7.12
+
+cd /lustre/durandk/HELICOVERPA/TREEMIX/Results/file_vcf2treemix_assulta
+
+# a faire ensuite 
+declare -A chrom_map=(
+    [NC_061482.1]="chr.31"
+    [NC_061481.1]="chr.30"
+    [NC_061480.1]="chr.29"
+    [NC_061479.1]="chr.28"
+    [NC_061478.1]="chr.27"
+    [NC_061477.1]="chr.26"
+    [NC_061476.1]="chr.25"
+    [NC_061475.1]="chr.24"
+    [NC_061474.1]="chr.23"
+    [NC_061473.1]="chr.22"
+    [NC_061472.1]="chr.21"
+    [NC_061471.1]="chr.20"
+    [NC_061470.1]="chr.19"
+    [NC_061469.1]="chr.18"
+    [NC_061468.1]="chr.17"
+    [NC_061467.1]="chr.16"
+    [NC_061466.1]="chr.15"
+    [NC_061465.1]="chr.14"
+    [NC_061464.1]="chr.13"
+    [NC_061463.1]="chr.12"
+    [NC_061462.1]="chr.11"  # Updated here
+    [NC_061461.1]="chr.10"
+    [NC_061460.1]="chr.9"
+    [NC_061459.1]="chr.8"
+    [NC_061458.1]="chr.7"
+    [NC_061457.1]="chr.6"
+    [NC_061456.1]="chr.5"
+    [NC_061455.1]="chr.4"
+    [NC_061454.1]="chr.3"
+    [NC_061453.1]="chr.2"
+    [NC_061452.1]="chr.1"
+)
+cp DATA_Helicoverpa_16122024_138samples_OUTGROUP.filtered.recode.vcf.gz /lustre/durandk/HELICOVERPA/TREEMIX/Results/file_vcf2treemix_assulta
+zcat DATA_Helicoverpa_16122024_138samples_OUTGROUP.filtered.recode.vcf.gz >> DATA_Helicoverpa_16122024_138samples_OUTGROUP.filtered.recode.vcf
+ 
+
+# Perform the replacements on the decompressed file
+for old_name in "${!chrom_map[@]}"; do
+    new_name="chr.${chrom_map[$old_name]}"
+    echo "Replacing $old_name with $new_name..."
+    sed -i "s/${old_name}/${new_name}/g" DATA_Helicoverpa_16122024_138samples_OUTGROUP.filtered.recode.vcf
+done
+#rename output vcf
+mv DATA_Helicoverpa_16122024_138samples_OUTGROUP.filtered.recode.vcf DATA_Helicoverpa_16122024_138samples_OUTGROUP.filtered.rename.vcf
+
+/storage/simple/projects/faw_adaptation/programs/vcftools_0.1.13/bin/vcftools \
+   --vcf DATA_Helicoverpa_16122024_138samples_OUTGROUP.filtered.rename.vcf \
+   --max-missing 1 \
+   --recode \
+   --out DATA_Helicoverpa_16122024_138samples_OUTGROUP.filtered.1.rename
+
+
+
+/lustre/durandk/HELICOVERPA/TREEMIX/SCRIPT/vcf2treemix.sh  DATA_Helicoverpa_16122024_138samples_OUTGROUP.filtered.1.rename.recode.vcf  /lustre/durandk/HELICOVERPA/TREEMIX/SCRIPT/pop_assulta.clust
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