mv instead of cp

juanjo255 · Oct 31, 2024 · ac7ff0e · ac7ff0e
1 parent 683ba5c
commit ac7ff0e
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/scripts/annotate_vcf.sh b/scripts/annotate_vcf.sh
@@ -13,17 +13,17 @@ annotate_vcf(){
     reference_annot=$exec_path"/refseqMT"
 
     bcftools annotate -a "$reference_annot/HV.bed"   $vcf_file -c "CHROM,FROM,TO,Hypervariable"  -h <(echo '##INFO=<ID=Hypervariable,Number=1,Type=String,Description="Hypervariable">') > $vcf_file_annot
-    cp $vcf_file_annot $vcf_file 
+    mv $vcf_file_annot $vcf_file 
     bcftools annotate -a "$reference_annot/HP.bed"    $vcf_file -c "CHROM,FROM,TO,Homopolymer"  -h <(echo '##INFO=<ID=Homopolymer,Number=0,Type=Flag,Description="Homoloplymer">') > $vcf_file_annot 
-    cp $vcf_file_annot $vcf_file
+    mv $vcf_file_annot $vcf_file
     bcftools annotate -a "$reference_annot/HS.bed"    $vcf_file -c "CHROM,FROM,TO,Hotspot"  -h <(echo '##INFO=<ID=Hotspot,Number=0,Type=Flag,Description="Hotspot">')              > $vcf_file_annot 
-    cp $vcf_file_annot $vcf_file
+    mv $vcf_file_annot $vcf_file
     bcftools annotate -a "$reference_annot/CDS.bed"   $vcf_file -c "CHROM,FROM,TO,CDS" -h <(echo '##INFO=<ID=CDS,Number=1,Type=String,Description="CDS">')                         > $vcf_file_annot 
-    cp $vcf_file_annot $vcf_file
+    mv $vcf_file_annot $vcf_file
     bcftools annotate -a "$reference_annot/RNR.bed"   $vcf_file -c "CHROM,FROM,TO,RNR"  -h <(echo '##INFO=<ID=RNR,Number=1,Type=String,Description="rRNA">')                       > $vcf_file_annot 
-    cp $vcf_file_annot $vcf_file
+    mv $vcf_file_annot $vcf_file
     bcftools annotate -a "$reference_annot/TRN.bed"   $vcf_file -c "CHROM,FROM,TO,TRN"  -h <(echo '##INFO=<ID=TRN,Number=1,Type=String,Description="tRNA">')                       > $vcf_file_annot 
-    cp $vcf_file_annot $vcf_file
+    mv $vcf_file_annot $vcf_file
     bcftools annotate -a "$reference_annot/DLOOP.bed" $vcf_file -c "CHROM,FROM,TO,DLOOP"  -h <(echo '##INFO=<ID=DLOOP,Number=0,Type=Flag,Description="DLOOP">')                    > $vcf_file_annot 
 
     ## Change name to old name