MAFtools variant classes mapping
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Entering edit mode
14 months ago
SunRise2019 ▴ 60

I would like to create a maf file from a variants data.frame, which uses different variant classes than those used by read.maf.

I have tried to map the variant classification classes in my data to those of MAFtools, but could not manage to map all variant classes. I am a student for bioinformatics with little molecular biology expertise. A google search could not give me clear guidance as how to proceed.

I would appreciate any help with mapping the following variants:

non_coding_exonic,
non_coding_intronic,
upstream_gene,
5_prime_UTR_intronic,
kozak_sequence,
downstream_gene,
stop_gained,
stop_retained,
initiator_codon,
3_prime_UTR_intronic,
stop_lost

... to the variants classes required by MAFtools:

Frame_Shift_Del,
Frame_Shift_Ins,
In_Frame_Del,
In_Frame_Ins,
Missense_Mutation,
Nonsense_Mutation,
Silent,
Splice_Site,
Translation_Start_Site,
Nonstop_Mutation,
3'UTR,
3'Flank,
5'UTR,
5'Flank,
IGR, 
Intron,
RNA,
Targeted_Region

Thanks very much.

variants mutations • 674 views
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I found the annovarToMaf script really useful for this - it shows some mapping:

http://annovar.openbioinformatics.org/en/latest/user-guide/gene/

https://rdrr.io/bioc/maftools/src/R/annovarToMaf.R

It might help to map each of the above to Sequence Ontology terms - that seems to be the gold standard.

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