What does this following maf column mean?
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?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Manual corrections for allele mismatches
written by Sakshi •
-
Different SNP at the at a position in vcf file compared to REF and ALT allele.
written by Abbas.M •
-
Reference genome, VCF files, genotype
written by tea.vuki •
-
Types of base substitutions
written by Gene_MMP8
-
Annotate genomic positions with dbSNP rsIds
written by Jimbou
-
How to extract only transition mutations/ SNPs from VCF file
written by sadsam •
-
Transitions and Transversions representation
written by onemoreuser •
-
identifying ref, alt allele and strand information
written by tonja.r
-
Inferring zygosity information from MAF
written by newDNASeqer
-
How To Detect And Query Poly-Allelic Snps?
written by Michael Dondrup
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
This is obtained from a pan cancer study path.
Can you please clarify what tumor_seq_allele_1/2 really mean?
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?
The maf file documentation doesn't clarify it either.