running time

README.md

 `--minDepthForLowMAPQ` 10, **Minimum read depth before a locus is considered a potential candidate for poorly mapped**
 We don't want to consider a site as POOR_MAPPING_QUALITY just because it has two reads, and one is MAPQ. We won't assign a site to the POOR_MAPPING_QUALITY state unless there are at least minDepthForLowMAPQ reads covering the site.
 
+##### Per sample running time 
+
+Settings:
+
+Disk size: 500
+
+Cluster: OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc
+
+sample: 30x WGS 
+
+2h30min

inputs

 {
-  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.disk_size": "400",
   "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:3.8-1",
   "{{ project_name }}.bam_index": "{{ bam_index }}",
   "{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc",
   "{{ project_name }}.bam": "{{ bam }}",
   "{{ project_name }}.sample": "{{ sample }}",
-  "{{ project_name }}.ref_dir": "{{ ref_dir }}"
+  "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
 }