diff --git a/Log/Update_summary.txt b/Log/Update_summary.txt deleted file mode 100644 index 073ea19..0000000 --- a/Log/Update_summary.txt +++ /dev/null @@ -1,25 +0,0 @@ -1. Name of the power point report script: -PRONTO (rePort geneRator fOr iNpred Tumor bOards) -2. All Clinical and meta data is stored in the file “InPreD_PRONTO_metadata.txt”. And the script will generate report for the samples with the column "Create_report==Y". -3. The filtered variants are read from the TSOPPI file “..._small_variant_table_forQC.tsv” (should be generated within TSOPPI in the next version, until then we rename the file manually). -If this file does not exist in the TSOPPI results folder, the script will read from the file "..._small_variant_table.tsv" instead. -4. The output results will be saved into a folder named with runID and the subfolder named with the DNA sample ID. -5. In the header to the right in PP report, it is printed “Clinical_diagnosis” (from the meta data file). If unavailable, the PCGR tumor type is printed on slide 4-7. -6. No “tumor type” is printed in the left grey box. -7. In the upper grey box on the left in PP report, print from the meta data file: “sex”, age (calculated from “Year_of_birth”), “Year_of_diagnosis” and “Requisition_hospital”. -8. Year in upper left is the same as the sequencing year (printed from the sequenced run id). -9. The script checks if there is a matching RNA in the “sample-list” file in TSOPPI. -Within the meta data file, it then looks for both DNA and RNA information in the column “Sample_material_id_PS”, and print on two lines as follows: DNA: “Sample_material_id_PS”, RNA: “Sample_material_id_PS”. -10. The printed text in the header is in white color. Blue header is behind the orange header. Darker color of the orange header. -11. Smaller text (size 9) for the Bio material; ex “primary tumor, post-treatment”. -12. Bigger text (size X) for RNA fusion and splice findings. -13. The script Does not print “N=xx» in the header in the table to the right. -14. Updated description on the first page: “Variants of uncertain significance (VUS) refer to variants with unknown/unclear/inconclusive/contradictory functional consequence in cancer. Level of evidence for experimental treatment follows ESCAT guidelines and will be defined by the respective study/trial.”. -Unclear is updated to uncertain in the sentence “Variant of uncertain significance (VUS)”. -15. Updated description of CN: “CN=copy number (assumes ploidy 2).” in slide 5 to 7. -16. Updates in the table slide 8: one column added with information from “change_summary”, and one column added with the MTB format. -17. New template with ctDNA info in the last slide. -18. Added "inpred_node=" in configure file, so that script will print the node name into the header of the Power point report automatically. -19. Bigger text (size 7) for the fusion text and the MS status in slide 2,6,7. -20. The text locations of the PP report on top right area are bit higher. -21. Updated description on the slide 6-7 right lower area: "#Variant of uncertain significance (VUS)".