MutSig2CV

MutSig2CV copied to clipboard

hg19 vs hg38 coverage model

1

I understand that the coverage_models_mat_file used for hg19 is coverage_models.v5a.mat and the hg38's is coverage_models.agilent.mat. However, I'm running into an error that longname and exon variables are not present in...

NigeI

Hi, I want to use the background mutation rates (BMRs) from MutSig2CV and I was wondering how to obtain those. I am currently looking at the output of MutSig2CV on...

uthsavc

The link to the MCR in the MutSig2CV README (and therefore this site) does not work, but the one that is in the reference file does work: http://www.mathworks.com/supportfiles/MCR_Runtime/R2013a/MCR_R2013a_glnxa64_installer.zip

toddajohnson

The params file format

4

Hello MutSig2CV Authors, In the instructions for param file it says that the example file is available in test/input/params.txt. but there is no test folder. I made a params_file.txt file...

RupalHatkar

Saving results... Reference to non-existent field 'longname'.

2

Hi getzlab team, I ran the MutSigCV2 for the hg38 samples with the following command: `bin/MutSig2CV ${MAF_FILE} ${OUTPUT_DIR} params.txt ` The params.txt follows the [default params for hg38 ](https://github.com/getzlab/MutSig2CV/issues/10#issuecomment-1142375852)with a...

yusufdjuanda

Error when I run MutSig2CV using hg38

1

Hi, when I run MutSig2CV using hg38 files like #10. There are some errors as below: ``` 1.000000 [ 1946 377 85 13 3 6 ] 04:51:57 04:51:57 19260/19260 ZZZ3...

lh12565

duplicate patients removed when I set params.txt not to do this

5

Dear MutSig2CV team, Even setting params.txt not to remove duplicate patients, my execution is doing that anyways. -------------------- MUTSIG_VERSION = 2CV v3.11 LOADING DATA Processing target list. Loading mutations... Keeping...

eltonjrv

Not found: reference/mutation_type_dictionary.v4.txt

9

Hello, We have downloaded hg38 reference files from: [gs://getzlab-mutsig2cv-reference-files/hg38](url) and have followed instructions shown in: [https://github.com/getzlab/MutSig2CV/issues/10](url) However, we still get the error: `Not found: reference/mutation_type_dictionary.v4.txt ` Could you please advise?...

ulloaa

Low number of significant mutations

2

I have a WGS cohort with 36 patients. When I run mutsig2cv with hg38 genome, I get only 5 genes with q

srithegreat

Ambiguous vesion difference & chrcount for build38

5

Hi there, **Q1. Ambiguous vesion difference** Threr are two pathes where I can download MutSig2CV, p1. link in readme: `http://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/MutSig2CV.tar.gz` p2. path on github: `https://github.com/getzlab/MutSig2CV/blob/master/bin/MutSig2CV` **MutSig2CV from p1 can't read...

RysBen