validation

inputs

@@ -9,7 +9,7 @@
   "{{ project_name }}.sample_name": "{{ sample_name }}",
   "{{ project_name }}.del_breakpoint": "oss://pgx-result/renluyao/manuscript_v3.0/difficult_region/Tier1.del.breakpoint",
   "{{ project_name }}.ins_breakpoint": "oss://pgx-result/renluyao/manuscript_v3.0/difficult_region/Tier1.ins.breakpoint",
-  "{{ project_name }}.sdf": "oss://pgx-reference-data/GRCh38.d1.vd1/GRCh38.d1.vd1.sdf/"
+  "{{ project_name }}.sdf": "oss://pgx-reference-data/GRCh38.d1.vd1/GRCh38.d1.vd1.sdf/",
   "{{ project_name }}.LINE": "oss://pgx-result/renluyao/manuscript_v3.0/difficult_region/LINE.3.bed",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
   "{{ project_name }}.LTR": "oss://pgx-result/renluyao/manuscript_v3.0/difficult_region/LTR.3.bed",

reform_vcf.sh

@@ -0,0 +1 @@
+for i in *vcf; do cat $i | grep -v '#' | sort -k1,1 -k2,2n | cut -f1-10 | grep -v '0/0' | grep -v '\./\.' | cat header - > $i.sorted.vcf; done