Gene Alias Issues in MutSigCV

[Angelussong]

Hi, 

I recently ran MutSigCV on GenePattern using a MAF file called by GATK Mutect2 followed by Funcotator under hg19. However, I found that some genes that seem statistically significant did not show up in the MutSigCV results such as ADGRV1 and KMT2C. 

When I went into the exome 192 coverage file (the default file for MutSigCV) I found that it has that gene but under different aliases. KMT2C is listed as MLL3 and ADGRV1 is listed as GPR98. As a matter of fact, I ran a small test on the gene symbols in the exome 192 coverage file and found a ton of genes which are aliases, therefore, couldn't match to my dataset. 

I am wondering if there is a way to fix this to make all the gene symbols consistent? 

Thanks, 

Hanbing Song

[Barbara Hill]

Hello Hanbing, 

Do you have a job id you can point us to? I think this may be a known issue, but I need to check the details to verify.

Thank you

-Barbara

[Angelussong]

Hi Barbara, 

The Job ID was 362000. But the job was from July 14th so I guess it's already deleted. 

Thanks, 

Hanbing

[Barbara Hill]

Ah - yes, then that would have been purged.

Do you still need assistance?

Best

-Barbara

[Angelussong]

Hi Barbara, 

I think I found a fix by mapping all the gene symbols in my datasets to the ones in MutSigCV so they are now compatible. 

Thanks, 

Hanbing

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