Fix VCF file names in output directories

submit_bcbio_trio_wes.sh

@@ -38,6 +38,12 @@ then
   do
     mv $OUTPUT_DIR/$INDV $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}/
   done
+
+  # fix VCF output file names
+  cd $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}
+  mv ${PROJECT_ID}${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz ${PROJECT_ID}_${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz
+  mv ${PROJECT_ID}${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz.tbi ${PROJECT_ID}_${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz.tbi
+
 else
   echo $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID} does not exist.
 fi