bim files

[DJon]

Hi Chris,

I got a set of bim, fam, bed files.

For some rsIDs, the 5th column of bim files contain '0'.

Eg:

0    rs2698846    0    0    0    G

0    rs35425675    0    0    A    T

0    rs3876241    0    0    0    T

0    rs160179        0    0    C    G

What does this '0' mean?  I need to calculate PRS, and do these '0' affect that?

There are some few 'D's and 'I's as well, I believe they are insertions and deletions. Will they affect PRS calculation?

If so what steps do I need to take?

Thanks.

DJon

[Christopher Chang]

1. A '0' allele code in a .bim file is usually a side-effect of conversion to/from a format (most commonly .ped+.map; this is one reason to stop using the .ped format whenever possible) which isn't able to store allele codes that don't appear in one of the samples.  You may need to use the --a1-allele/--a2-allele flags to recover this information from another file that still has the information.

2. While it should be possible to translate most or all 'D'/'I' allele codes into VCF-style encoding, I'm not aware of a public resource that makes this easy.  If necessary, you can use "--snps-only just-acgt" to filter out those variants.