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Calculating TMB for TCGA data
written by Jaber •Hi, community, I am facing a bit of a struggle to find the genomic region in Mb for the TMB calculations, I am using the …
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How to calculate tumor mutation burden (TMB)?
written by tanbiswas6 •Hi I've tumor-normal WES data and I've analyzed data using GATK-Mutect2 pipeline to call somatic mutations. Now can anyone let me know hoe to calculate …
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Tumor Mutation Burden
written by adarsh •Hello, I need to calculate the Tumor Mutation Burden for a Comprehensive Cancer Panel after calling the variants. Is there any specific tool to do …
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Tumour mutation burden vs mutant cells ratio vs Variant allele fraction
written by whb •What I understand is Tumor mutation burden (TMB) is `number of unique mutation in a sample`/ `the size of the capture` and variant allele fraction …
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How to calculate TMB for somatic data TCGA
written by NT •Hi, I have to calculate for the first time the tumor mutational burden (TMB) for each sample of a big maf file of TCGA (https://gdc.cancer.gov/about-data/publications/mc3-2017) …
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How to classify samples into high and low Tumor mutational burden?
written by newbieI actually wanted to calculate TMB (tumor mutational burden) for TCGA breast cancer samples. But I see that mutational load is available here [Mutation Load …
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How to calculate Tumor Mutation Burden (TMB) for TCGA samples
written by MikeHi All, What is difference between "Tumor Mutation Burden (TMB)" and "mutational load" ? I have mutation matrix for TCGA samples (generated from maftools, see …
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question about mutation data from TCGA
written by tujuchuanliI want to download and analyze the mutation data of TCGA. I find that the mutation data is controlled on original download source (https://portal.gdc.cancer.gov/repository). I …
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Can anyone help me to confirm the number of matched tumor and normal samples in TCGA-BRCA?
written by Wen Wang •Hi all, I was looking at the somatic mutation summary at GDC data portal. It seems there are 986 samples with matched tumor and normal …
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Tumor Mutation Burden calculation: all_mut vs non_synonym
written by ptintoFor Tumor Mutation Burden (TMB) usually people calculates non_synonym_mutations / Mb. In this Ilumina's tech report (https://www.illumina.com/content/dam/illumina-marketing/documents/products/whitepapers/trusight-tumor-170-tmb-analysis-white-paper-1170-2017-001.pdf) they calculate TMB for TruSight Tumor 170 with …