diff annovar_yaml/YAML_arguments_annovar.yml @ 5:856448f167da draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annovar_yaml/YAML_arguments_annovar.yml	Mon May 13 06:37:39 2019 -0400
@@ -0,0 +1,111 @@
+GENERAL:
+  - APPLICATION: 'annovar'
+    PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
+    CODING_ANNOVAR: 'coding_annovar.pl '
+    TABLE_ANNOVAR: 'table_annovar.pl '
+    LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
+    DOT2UNDERLINE:
+      yes: '--dot2underline '
+      no: ''
+    NASTRING: '--nastring . '
+    OTHERINFO:
+      yes: '--otherinfo '
+      no: ''
+    POLISH:
+      yes: '--polish '
+      no: ''
+    REMOVE:
+      yes: '--remove '
+      no: ''
+    THREAD: '--thread 8 '
+    INPUTFORMAT:
+      vcfinput: '--vcfinput '
+    SPECIES:
+      human: 'humandb '
+      mouse: 'mousedb '
+    BUILD: '--buildver hg19 '
+ANALYSIS:
+  DATABASES:
+    - NAME: 'cosmic84'
+      PROTOCOL: 'cosmic'
+      VERSION: '84'
+      COMMENT: '20190221' 
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'f'
+      COLSWANTED: '--colswanted 4 '
+    - NAME: 'refgene19'
+      PROTOCOL: 'refgene'
+      VERSION: '19' 
+      COMMENT: '20190210'  
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'g'
+      HGVS:
+        yes: '--hgvs '
+        no: ''
+      SPLICING: '--splicing 6 '
+      EXONSPLIC:  
+        yes: '--exonicsplicing '
+        no: ''
+    - NAME: 'ncbiRefSeq_UMCU'
+      PROTOCOL: 'ncbiRefSeq'
+      VERSION: '_UMCU'
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      COMMENT: "100519"
+      OPERATION: 'g'
+      HGVS:
+        yes: '--hgvs '
+        no: ''
+      SPLICING: '--splicing 6 '
+      EXONSPLIC:
+        yes: '--exonicsplicing '
+        no: ''
+    - NAME: 'avsnp150'
+      PROTOCOL: 'avsnp'
+      VERSION: '150'
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'f'
+      COLSWANTED: '--colswanted 1 '
+    - NAME: 'clinvar_20180603'
+      PROTOCOL: 'clinvar'
+      VERSION: '_20180603'
+      COMMENT: 'blah'
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'f'
+      COLSWANTED: '--colswanted 5 '
+    - NAME: 'class100519'
+      PROTOCOL: 'class'
+      VERSION: '100519'
+      AVAILABLE:
+        yes: '1'
+        no: '0'
+      REQUIRED:
+        yes: '1'
+        no: '0'
+      OPERATION: 'f'
+      COLSWANTED: '--colswanted 1 '
+