Ambiguous vesion difference & chrcount for build38

[RysBen]

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 the third parameter, i.e., params.txt, for example, my params.txt looks like,

mutation_blacklist_file	none
skip_permutations	true
exclude_noncoding	1
enforce_target_list	1
mutation_type_dictionary_file	/path/reference/mutation_type_dictionary.v5.txt
context_and_effect_categs_file	/path/reference/context_and_effect.c65e29b.txt
basewise_coverage_fwb_file	/path/reference/coverage_basewise.fwb
conservation_fwb_file	/path/reference/conservation46.fwb
FixedWidthBinary_jar_file	/path/reference/FixedWidthBinary.jar
context_and_effect_fwb_file	/path/reference/hg38/context_and_effect_track.fwb
coverage_models_mat_file	/path/reference/hg38/coverage_models.agilent.mat
target_list_file	/path/reference/hg38/target_list.gencode25.txt
covariates_file	/path/reference/hg38/covariates.agilent.txt
build	hg38

my command looks like:

./MutSig2CV test.maf out_dit params.txt
#...
#Not found: reference/mutation_type_dictionary.v4.txt
#...

from output, mutation_type_dictionary_file was not mutation_type_dictionary.v5.txt specified in params.txt, but mutation_type_dictionary.v4.txt default.

Q2. Don't know how to find chrcount for build hg38 When I used MutSig2CV from p2, params.txt was passed as excepted. But some error happend as below:

Mutation file contains multiple columns for newbase info:
Tumor_Seq_Allele2
newbase          
Will use newbase
Scanning for duplicate patients...
Comparing on the basis of coding mutations only...
convert_chr: assuming human for chrX/chrY
0 patients involved in an overlap.
Loading coverage models ... 1 scheme(s).
Enforcing target list.
Mapping mutations to targets: Error using get_chrcount (line 63)
Don't know how to find chrcount for build /path/reference/hg38/

It seems get_chrcount.m can't recognized hg38.

Any suggestion on which version to use or how to work around hg38 error?

[RysBen]

After removing the last line build hg38, the Don't know how to find chrcount error no longer appears

mutation_blacklist_file	none
skip_permutations	true
exclude_noncoding	1
enforce_target_list	1
mutation_type_dictionary_file	/path/reference/mutation_type_dictionary.v5.txt
context_and_effect_categs_file	/path/reference/context_and_effect.c65e29b.txt
basewise_coverage_fwb_file	/path/reference/coverage_basewise.fwb
conservation_fwb_file	/path/reference/conservation46.fwb
FixedWidthBinary_jar_file	/path/reference/FixedWidthBinary.jar
context_and_effect_fwb_file	/path/reference/hg38/context_and_effect_track.fwb
coverage_models_mat_file	/path/reference/hg38/coverage_models.agilent.mat
target_list_file	/path/reference/hg38/target_list.gencode25.txt
covariates_file	/path/reference/hg38/covariates.agilent.txt

[yusufdjuanda]

Hi, I am currenlty planning on using MutSigCV based on hg38 reference genome. I am wondering where you get the hg38 reference files listed in the params.txt you mentioned?

Thanks!

[RysBen]

Hi yusufdjuanda,

I downloaded hg38 files by the google cloud. Here was the commmand.

gsutil -m cp -r gs://getzlab-mutsig2cv-reference-files/hg38 /local/path/

[yusufdjuanda]

Thanks @RysBen for the prompt response, I also wonder if you happen to know any documentation regarding using hg38 ref genome for mutsigcv2 .

[julianhess]

Hi @yusufdjuanda,

Please see the following instructions for hg38 usage: https://github.com/getzlab/MutSig2CV/issues/10#issuecomment-1142375852