Pan5244

Bedmaker/Pan5244/Pan5244_CNV_query.json

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+{
+  "assembly": "GRCh37",
+  "coordinates": "",
+  "identifiers": "NM_002485.4",
+  "include3UTR": false,
+  "include5UTR": false,
+  "padding_3": 0,
+  "padding_5": 0,
+  "settings": {
+    "bed_type": "cnv",
+    "include_3utr": false,
+    "include_5utr": true,
+    "padding": {
+      "snp": 0,
+      "standard": 0
+    }
+  },
+  "snp_padding_3": 0,
+  "snp_padding_5": 0,
+  "use_separate_snp_padding": false,
+  "created_date": "06/03/2025, 12:28",
+  "updated_date": "06/03/2025, 12:28",
+  "submitter": "test"
+}

Bedmaker/Pan5244/Pan5244_Logfile.md

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+## Pan5244
+
+CP2 Exomedepth CNV calling BED file (build37) for R259
+
+# Request form for R259
+Pan5244_R259_bedrequest.txt was used  (added into mokabed/LiveBedfiles/RequestForms)
+
+5UTR was included for all genes and no padding was used. No additional sites were added. 
+
+# Run Bedmaker
+Pan5244_CNV_query.json contains the original query given to bedmaker to generate the bedfile.
+
+# Testing
+Pan5244_CNV.bed was tested in DNAnexus using ED_cnv_calling_v1.4.0. The app completed successfully without any error.

Bedmaker/Pan5244/Pan5244_cnv.bed

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+8	90947809	90947840	NBN;NM_002485.4
+8	90949254	90949303	NBN;NM_002485.4
+8	90955481	90955594	NBN;NM_002485.4
+8	90958368	90958523	NBN;NM_002485.4
+8	90960052	90960120	NBN;NM_002485.4
+8	90965472	90965919	NBN;NM_002485.4
+8	90967511	90967783	NBN;NM_002485.4
+8	90970953	90971082	NBN;NM_002485.4
+8	90976638	90976735	NBN;NM_002485.4
+8	90982592	90982785	NBN;NM_002485.4
+8	90983401	90983518	NBN;NM_002485.4
+8	90990448	90990551	NBN;NM_002485.4
+8	90992962	90993121	NBN;NM_002485.4
+8	90993603	90993751	NBN;NM_002485.4
+8	90994950	90995083	NBN;NM_002485.4
+8	90996753	90996899	NBN;NM_002485.4

LiveBedfiles/RequestForms/Pan5244_R259_bedrequest.txt

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+THIS FORM SHOULD BE USED TO REQUEST THE CREATION OF NEW BED FILES				
+"All requests should be emailed to the bioinformatics team ([email protected]) using the subject ""BED File Creation Request"""				
+Please ensure that gene symbols/transcripts for the request have been added to a panel in Moka before submission				
+
+"PLEASE USE ROW C TO FILL IN ANY REQUESTED DETAILS. IF N/A, LEAVE FIELD BLANK"				
+
+Name	Full name of requestor	Rebecca Haines	Full name of checker	Heidi Kuoppamaa
+Date	Date in DD/MM/YYYY format	20/02/2025		28/02/2025
+Email	Email address to receive confirmation			
+
+
+Pan number	Pan number for BED file to be created	Pan5244		
+Panel description	Description of the panel and purpose of the BED file	R259 CNV calling BED		
+Assembly	GRCh37 or GRCh38	GRCh37		
+Identifiers	"Please enter the list of identifiers to be used (transcript ID, rsID, HGNC). Version MUST be included"	see below		
+Padding	"Describe the padding type and the number of base pairs required (i.e., exons +10, SNPs +5)"	none		
+UTR inclusion	3'/5' UTRs to be included?	5'UTR		
+Additional sites	"Provide a list of coordinates for any additional target regions with padding included, Format chr1:10000-20000 or 1-10000-20000. OR provide BED file to use"	none		
+
+Identifiers				
+NBN	NM_002485.4