UCSC MAF format left or right align gaps?

Question

[jxmavs]

Hello,

Does anyone know if the MAF format have a convention of right or left aligning its gaps/indels as seen in VCF files (where an indel is always left-aligned)?. I generated my own multiple sequence alignment using the multiz pipeline from UCSC and found that in some cases a gap is right aligned, in other cases its left aligned.

What I mean is the following, assume that I have 3 sequences, looking only at the sequence part in the MAF format,

A- TTA

A- TTA

ATTTA

In this case the gap is left aligned, if it was right aligned, I would see the following:

ATT -A

ATT -A

ATTTA

In my MAF formats, I see both instances occurring, which makes me wonder if there is a set convention or not. If there isn't, I would also appreciate any references on tools which can left align these gaps in the sequence file if there are any available.

Answer 1

[Kevin Blighe]

It is likely something that was 'looked over' during the processing of the data, i.e., some labs performed left-alignment, while others did not. It's notable, too, that different labs used different variant callers for the data. So, the MAF Level 3 [open access] TCGA data is a real mixed bag and needs to be used with utmost caution.

Your post is 3 years old, so, perhaps this situation has been improved, now that the TCGA consortium has 'harmonised' all of their data.

Kevin