diff --git a/Bedmaker/Pan5244/Pan5244_CNV_query.json b/Bedmaker/Pan5244/Pan5244_CNV_query.json new file mode 100644 index 00000000..db9c266d --- /dev/null +++ b/Bedmaker/Pan5244/Pan5244_CNV_query.json @@ -0,0 +1,24 @@ +{ + "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" +} \ No newline at end of file diff --git a/Bedmaker/Pan5244/Pan5244_Logfile.md b/Bedmaker/Pan5244/Pan5244_Logfile.md new file mode 100644 index 00000000..6919b457 --- /dev/null +++ b/Bedmaker/Pan5244/Pan5244_Logfile.md @@ -0,0 +1,14 @@ +## 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. \ No newline at end of file diff --git a/Bedmaker/Pan5244/Pan5244_cnv.bed b/Bedmaker/Pan5244/Pan5244_cnv.bed new file mode 100644 index 00000000..4e50ce38 --- /dev/null +++ b/Bedmaker/Pan5244/Pan5244_cnv.bed @@ -0,0 +1,16 @@ +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 \ No newline at end of file diff --git a/LiveBedfiles/RequestForms/Pan5244_R259_bedrequest.txt b/LiveBedfiles/RequestForms/Pan5244_R259_bedrequest.txt new file mode 100644 index 00000000..c2c40c9c --- /dev/null +++ b/LiveBedfiles/RequestForms/Pan5244_R259_bedrequest.txt @@ -0,0 +1,21 @@ +THIS FORM SHOULD BE USED TO REQUEST THE CREATION OF NEW BED FILES +"All requests should be emailed to the bioinformatics team (gstt.mokaguys@nhs.net) 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