What does this following maf column mean?

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6.5 years ago

Gene_MMP8 ▴ 240

I was trying to query a maf file based on variants when I came across two columns: tumor_seq_allele_1 and tumor_seq_allele_2. Now I found out that these two columns are not identical. Also, I know that alleles are different version of the same gene. So what can I say about the variant?
Eg:

Ref: C
Tumor_seq_allele_1: C
Tumor_seq_allele_2: T
______________________
Ref: G
Tumor_seq_allele_1: G
Tumor_allele_allele_2=A

So what can I say about the variant in both cases? That the first case, there are C>T transitions and in the second, G>A transition?

R sequencing • 2.0k views

ADD COMMENT • link 6.5 years ago by Gene_MMP8 ▴ 240

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Where did you obtain this file from? I've seen this format in TCGA, but in my dataset all allele_1 alleles were the same as Ref Alleles

ADD REPLY • link 6.5 years ago by Ram 44k

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This is obtained from a pan cancer study path.

ADD REPLY • link 6.5 years ago by Gene_MMP8 ▴ 240

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Can you please clarify what tumor_seq_allele_1/2 really mean?

ADD REPLY • link 6.5 years ago by Gene_MMP8 ▴ 240

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I'm not really sure. I thought it was just Ref and Alt myself, but I guess I was wrong? Or maybe tumors can have both alleles change at a location, given tumors from one person need not be the same genotype?