No block substitutions in plink BIM file?
Entering edit mode
8 weeks ago
BioStar123 • 0

The BIM file from PLINK contains the variant information that accompanies a BED file. The variants called are based on exome sequencing. However, I encounter a strange issue. The BIM file consists of only single nucleotide substitutions, insertions, and deletions of base pairs. There are 0 multiple base pair substitutions. (block substitutions)

Is this normal?

I copied a few lines from one of the BIM files. (variant 1 is ALT, and 2 is REF)

11  11:75423892:G:C 0   75423892    C   G
11  11:75423898:I:1 0   75423898    CA  C
11  11:75423899:D:3 0   75423899    A   AGTG
11  11:75423899:A:G 0   75423899    G   A
11  11:75423912:C:G 0   75423912    G   C
plink bim • 215 views

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