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## Need
### TMB calculation today in BALSAMIC
The current definition is based on:
1. TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome …
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Dear Professors@wtwt5237:
Recently,I have been learning this pipeline,and hope to transplant it in our own data.However,I have some questions about the input data in the somatic.pl.Why you set …
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I am trying to demultiplex tumor samples using genotype data from healthy cells, and demuxlet is calling the majority of my tumor cells doublets. I'm looking for any insight about whether somatic muta…
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Hello,
I am trying to get somatic mutations from `speedseq somatic` but it has been more than 24 hours but it is still running and no output is generated. Here is the command I am using:
tim…
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Dear professors@tianshiliu,
Recently,I am very interested in your work for lineage tracing use this SClineager package.I use your test data in the data folder，which is the coverage.txt and the …
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I am currently working on a tumor bulk RNA-seq data set in order to identify somatic mutations. I have the BAM file for the tumor data set but I do not have the BAM file for a normal sample. Is there …
ghost updated
2 years ago
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Hello!
I am using strelka2 for calling indels. The indels called by other software and strelka1 all look normal. However, when I look into the output of strelka2, all variants have either very high…
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This ticket is for tracking the progress of the concordance project described here which is in collaboration with @davidbenjamin from DSP. The output of GATK Mutect2 is in VCF format, and there is an …
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**Background**:
Different cancers have different mutation burdens. One nice way to visualize them is the so-called hamburger plot. In the figure below as discribed in [this paper](http://www.natur…
jjgao updated
4 years ago
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1. Sometimes after running AA and getting ecDNAs, we also want to find some somatic mutations or allele-based CNA and so on, so the RG tag in bam is mostly important ! In order to reuse the bam file f…