MutsigCV about getzlab-pcawg-mutsig2cv_nc

[hurrialice]

Hi,

Have you downloaded "all.fwb" and "all.fwi" from the bucket gs://getzlab-pcawg-mutsig2cv_nc/ as mentioned here?

[julianhess]

Hi @Gtt19920502,

It seems that you're trying to run the original 2010 MutSigCV algorithm. This repo contains the release of MutSig2CV specifically for noncoding element analysis.

Rather than trying to get MutSigCV to work, it will be much easier to use the latest release of MutSig2CV for coding elements, which supersedes the original MutSigCV.

Please download that here: http://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/MutSig2CV.tar.gz

Note that it is a large download (~3 GB), since it includes all necessary reference files. Installation instructions are provided in the README.txt file. In addition to the MutSig executable, you will also need the MATLAB runtime environment, available here: http://www.mathworks.com/supportfiles/MCR_Runtime/R2013a/MCR_R2013a_glnxa64_installer.zip

[Gtt19920502]

Hi @Gtt19920502,

It seems that you're trying to run the original 2010 MutSigCV algorithm. This repo contains the release of MutSig2CV specifically for noncoding element analysis.

Rather than trying to get MutSigCV to work, it will be much easier to use the latest release of MutSig2CV for coding elements, which supersedes the original MutSigCV.

Please download that here: http://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/MutSig2CV.tar.gz

Note that it is a large download (~3 GB), since it includes all necessary reference files. Installation instructions are provided in the README.txt file. In addition to the MutSig executable, you will also need the MATLAB runtime environment, available here: http://www.mathworks.com/supportfiles/MCR_Runtime/R2013a/MCR_R2013a_glnxa64_installer.zip

Hi Julianhess,

Thank you very much for your reply and informations. I think maybe something wrong with my input file. I'll try it according your suggestion. Thank you very much.

[Gtt19920502]

Hi,

Have you downloaded "all.fwb" and "all.fwi" from the bucket gs://getzlab-pcawg-mutsig2cv_nc/ as mentioned here?

Hello,

Thank you very much for your reply. I used the MutSigCV 1.3 software. I'm not whether my input file is wrong? Thank you very much. The following one is my input. Could you please help me th check it whether it's right or not? Thank you very much.
Hugo_Symbol Tumor_Sample_Barcode Variant_Classification Chromosome Start_position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
A1CF LM-BN-1 3'UTR 10 52563029 GT G G
A1CF LM-BN-4 3'UTR 10 52563029 GT G G
A1CF LM-BN-5 3'UTR 10 52566432 CT C C
A2M LM-BN-1 Intron 12 9220823 G GA GA
A2M LM-BN-4 Intron 12 9220823 G GA GA
A2ML1 LM-BN-1 3'UTR 12 9028242 T C C
A2ML1 LM-BN-1 3'UTR 12 9028264 G A A
AAAS LM-BN-1 Missense_Mutation 12 53715218 G A A
AACS LM-BN-1 5'UTR 12 125586335 TG CA CA
AACS LM-BN-2 5'UTR 12 125607905 A G G
AACS LM-BN-2 5'UTR 12 125607960 C G G
AACS LM-BN-3 5'UTR 12 125586308 CTT C C
AACS LM-BN-3 5'UTR 12 125586308 CTT CTTT CTTT
AACS LM-BN-4 5'UTR 12 125586308 CT C C
AACS LM-BN-4 5'UTR 12 125586308 CT CTT CTT
AACS LM-BN-1 5'UTR 12 125586359 G C C
AADACL3 LM-BN-1 3'UTR 1 12787881 G A A
AADACL3 LM-BN-1 Missense_Mutation 1 12785945 A T T
AADAT LM-BN-3 3'UTR 4 170981506 TAAAAGTAGA T T
AAED1 LM-BN-4 3'UTR 9 99402375 C CA CA
AAED1 LM-BN-1 Missense_Mutation 9 99413690 C T T
AAGAB LM-BN-4 3'UTR 15 67493515 CT C C
AAGAB LM-BN-5 3'UTR 15 67493515 CT C C
AAGAB LM-BN-5 3'UTR 15 67493515 CT CTT CTT
AAK1 LM-BN-1 3'UTR 2 69688727 A AT AT
AAK1 LM-BN-2 3'UTR 2 69709361 G A A
AAK1 LM-BN-3 3'UTR 2 69688631 CA C C
AAK1 LM-BN-3 3'UTR 2 69688631 CA CAA CAA
AAK1 LM-BN-3 3'UTR 2 69702102 T TCCCCCCC TCCCCCCC

[Gtt19920502]

Yeah, It shows closed. I'll send the input now. Could you please tell me can you check it? Thank you very much. Hugo_Symbol Tumor_Sample_Barcode Variant_Classification Chromosome Start_position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 A1CF LM-BN-1 3'UTR 10 52563029 GT G G A1CF LM-BN-4 3'UTR 10 52563029 GT G G A1CF LM-BN-5 3'UTR 10 52566432 CT C C A2M LM-BN-1 Intron 12 9220823 G GA GA A2M LM-BN-4 Intron 12 9220823 G GA GA A2ML1 LM-BN-1 3'UTR 12 9028242 T C C A2ML1 LM-BN-1 3'UTR 12 9028264 G A A AAAS LM-BN-1 Missense_Mutation 12 53715218 G A A AACS LM-BN-1 5'UTR 12 125586335 TG CA CA AACS LM-BN-2 5'UTR 12 125607905 A G G AACS LM-BN-2 5'UTR 12 125607960 C G G AACS LM-BN-3 5'UTR 12 125586308 CTT C C AACS LM-BN-3 5'UTR 12 125586308 CTT CTTT CTTT AACS LM-BN-4 5'UTR 12 125586308 CT C C AACS LM-BN-4 5'UTR 12 125586308 CT CTT CTT AACS LM-BN-1 5'UTR 12 125586359 G C C Thanks julianhess <[email protected]> 于2020年7月13日周一 下午7:02写道：

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Closed #4 <#4>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQH2D3DGF2MO4FJEETBYYDDR3OOCPANCNFSM4OY2CIIA> .

[hurrialice]

Hi @Gtt19920502 ,

It seems that you are still using MutSigCV. If so, please use MutSig2CV downloaded as @julianhess described. MutSigCV on GenePattern is not up-to-date and will not be further supported.

Your input file seems okay. If you are still encountering problems with MutSIg2CV, please attach the log with your reply here.

Thanks!

[Gtt19920502]

Hello Qing, Thank you very much for your reply. I will try to do it using MutSig2CV. Thanks! qing zhang <[email protected]> 于2020年7月17日周五 上午9:01写道：

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Hi @Gtt19920502 <https://github.com/Gtt19920502> , It seems that you are still using MutSigCV. If so, please use *MutSig2CV* downloaded as @julianhess <https://github.com/julianhess> described. MutSigCV on GenePattern is not up-to-date and will not be further supported. Your input file seems okay. If you are still encountering problems with *MutSIg2CV*, please attach the log with your reply here. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQH2D3HEA5U633XFR3QWLYTR4BKTPANCNFSM4OY2CIIA> .

[Gtt19920502]

Hello Qing, The following one is the result of running MutSig2CV. It also shows error. Could you please tell me how to revise: [image: image.png] Thanks qing zhang <[email protected]> 于2020年7月17日周五 上午9:01写道：

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Hi @Gtt19920502 <https://github.com/Gtt19920502> , It seems that you are still using MutSigCV. If so, please use *MutSig2CV* downloaded as @julianhess <https://github.com/julianhess> described. MutSigCV on GenePattern is not up-to-date and will not be further supported. Your input file seems okay. If you are still encountering problems with *MutSIg2CV*, please attach the log with your reply here. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQH2D3HEA5U633XFR3QWLYTR4BKTPANCNFSM4OY2CIIA> .

[Gtt19920502]

Hello Qing, The following one is the result of running MutSig2CV. It also shows error. Could you please tell me how to revise: -/MntsigGV/mutsig2cv$。/Mutsig2CV II-MAF, mat outputWarning: latest version of matlab app-defaults file not foundContact your system administrator to have this file installedMUTSIG VERSION E 2cv3.11 LOADING DATA Processing target list oading mutations Mutation file contains multiple columns for newbase info Tumor_seq Allele newbase ill use newbase Mutation file is missing a column named one of the following: classification Variant_Type Error using Mutsig_2CV_v3_11_core(line 169) Mutation file missing classification column Error in Mutsig-_2cV_v3_11 wrapper(line 50) Thanks qing zhang <[email protected]> 于2020年7月17日周五 上午9:01写道：

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Hi @Gtt19920502 <https://github.com/Gtt19920502> , It seems that you are still using MutSigCV. If so, please use *MutSig2CV* downloaded as @julianhess <https://github.com/julianhess> described. MutSigCV on GenePattern is not up-to-date and will not be further supported. Your input file seems okay. If you are still encountering problems with *MutSIg2CV*, please attach the log with your reply here. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQH2D3HEA5U633XFR3QWLYTR4BKTPANCNFSM4OY2CIIA> .

[hurrialice]

HI @Gtt19920502

The error message is self-explanatory. Consider revising your table by changing column names, one example table would be

$ head /demo-mount/M2_refs/MC3.maf 
chr	pos	gene	ref_allele	newbase	type	classification	patient
1	13308		T	G	IGR	SNP	11D-09
1	13372		G	T	IGR	SNP	11D-08
1	13501		G	A	IGR	SNP	11D-08
1	13515		C	A	IGR	SNP	01D-08
1	13516		C	A	IGR	SNP	01D-08
1	13516		C	A	IGR	SNP	12D-09

MutSig2CV only expects 1 column of alt allele.

[julianhess]

You need to add a field for the "Variant_Type," which is described here: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/

[Gtt19920502]

Hi Julian, Thank you very much for your reply. I get it. I'll add the "Variant_Type" and try it again. Thanks julianhess <[email protected]> 于2020年7月18日周六 下午8:10写道：

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You need to add a field for the "Variant_Type," which is described here: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/ — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQH2D3GTKHBNA5NYPJ3TRNDR4JBZPANCNFSM4OY2CIIA> .

[Gtt19920502]

Hello Qing, Thank you very much for your reply. I get it. I'll revise it and try it again. Thanks qing zhang <[email protected]> 于2020年7月18日周六 下午8:06写道：

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HI @Gtt19920502 <https://github.com/Gtt19920502> The error message is self-explanatory. Consider revising your table by changing column names, one example table would be $ head /demo-mount/M2_refs/MC3.maf chr pos gene ref_allele newbase type classification patient 1 13308 T G IGR SNP 11D-09 1 13372 G T IGR SNP 11D-08 1 13501 G A IGR SNP 11D-08 1 13515 C A IGR SNP 01D-08 1 13516 C A IGR SNP 01D-08 1 13516 C A IGR SNP 12D-09 MutSig2CV only expects 1 column of alt allele. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQH2D3CMTRJSUMTFS6UX3CLR4JBKHANCNFSM4OY2CIIA> .