Update README.md

README.md

@@ -110,7 +110,9 @@ Any variant caller which can support regions specific variant calling can be int
 cd /mnt/fs_shared
 sudo singularity pull  docker://dancooke/octopus
 ```
-2. Run the following command inside GCP console by changing `--vcaller` to `Octopus`:
+2. Repeat part `1` and `2`
+3. Run the following command inside GCP console by changing `--vcaller` to `Octopus`:
 ```
 gcloud dataproc jobs submit pyspark --region=us-central1 --cluster=cluster-555  --properties=spark.pyspark.python=/usr/bin/python3.6,spark.pyspark.driver.python=/usr/bin/python3.6,spark.executor.memory=2G,spark.driver.memory=2G,spark.num.executors=3,spark.executor.cores=8  gs://bucket_taha_pk/scripts/bwa.py -- --part 3 --ref /mnt/fs_shared/reference/GRCh38.fa  --path /mnt/fs_shared/query/HG003/  --nodes 3 --cores 8 --aligner BWA --vcaller Octopus
 ```
+4. Repeat part `4` for merging VCFs and generating accuracy results using `hap.py`