23andme: Convert Human Assembly Build 36 to Build 37

Question

[samorjoy]

I obtained a bunch of snp Array data from the 23andme website. The raw data output looks like this. I want to convert it from human reference build 36 to human reference build 37. I know one solution is to convert it with Liftover.

Liftover requires the format to be in bed format. I converted the file raw data into bed format but notice that the raw data output from 23andme does not have a chromosome start and chromosome end. So what I did was use the position as the chromosome start and chromosome end.

Once I obtained the bed file, I tried running the Liftover command to convert from build 36 to build 37

./liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed

It runs fine but nothing appears in the output.bed file. The chain file is not picking up the snp location so it's not working properly.

Does anyone know how I can convert the output from 23andme into build 37? thanks

[Martombo]

if in a bed file the chromStart and chromEnd are the same, the length of the defined interval is 0. that means that you need to write in your bed file something like position-1 as chromStart and position as chromEnd (since bed files are 0-based)

[komal.rathi]

From the UCSC FAQs:

If you submit data to the browser in position format (chr#:##-##), the browser assumes this information is 1-based. If you submit data in any other format (BED (chr# ## ##) or otherwise), the browser will assume it is 0-based. You can see this both in our liftOver utility and in our search bar, by entering the same numbers in position or BED format and observing the results. Similarly, any data returned by the browser in position format is 1-based, while data returned in BED format is 0-based.

So, you need to +1 to the end position if your format is chr# ## ## because in this format, the browser will assume that the input is 0-based start and 1-based end.

An example is given here.

[Neilfws]

Just to address one point: chromStart and chromEnd is the position of the feature, not the chromosome start or end. This is stated in the definition of those terms on the page to which you linked.

[Ann]

Once you have made a converted file, would you mind sharing it - maybe using github or bitbucket?