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kyizhak / RNA_MUTECT_1.0

BSD 3-Clause "New" or "Revised" License
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Error while using FilterRNAMutationsNoPoN #6

Open sawantaniket461 opened 4 years ago

sawantaniket461 commented 4 years ago

Hi, I am a novice to Matlab. While using FilterRNAMutationsNoPoN script for some data analysis, the tool throws following error: convert_chr: assuming human for chrX/chrY convert_chr: assuming human for chrX/chrY Realignment filter Write interim maf file Load RNA editing structs Non-coding filtering RNA editing and EXAC filtering IG and pseudogene filtering Reference to non-existent field 'i_gene_type'.

Error in FilterRNAMutationsNoPoN (line 125)

Please suggest

longqh3 commented 4 years ago

Hi, I am a novice to Matlab. While using FilterRNAMutationsNoPoN script for some data analysis, the tool throws following error: convert_chr: assuming human for chrX/chrY convert_chr: assuming human for chrX/chrY Realignment filter Write interim maf file Load RNA editing structs Non-coding filtering RNA editing and EXAC filtering IG and pseudogene filtering Reference to non-existent field 'i_gene_type'.

Error in FilterRNAMutationsNoPoN (line 125)

Please suggest

Hi, I also encountered this problem and it suggested that the 'i_gene_type' column is missing in your maf file. I used Funcotator within GATK suite to get maf file and used sed software to repalce 'HGNC_Locus_Group' with 'i_gene_type' to fulfill its requirement. Hope it helps!

khushi0810 commented 1 year ago

Hello, I was getting the same error before and as suggested I changed HGNC_Locus_Group to i_gene_type but now I am encountering the following error Error using intersect Inputs A and B must be matrices with the same number of columns in the 'rows' case.

Error in intersect

Error in ExacPlusEditingFiltering (line 6)

Error in FilterRNAMutationsNoPoN (line 115)

MATLAB:INTERSECT:AandBColnumAgree

Do you have any idea how to go about this ?

Thank you !