PLINK ERROR: Could not place marker for left window edge

Question

[Aishwarya.Kulkarni]

I am using a following command

plink --noweb --bfile hapmap1 --recode --filter-controls --chr 1 --from-bp 3721218 --to-bp 3721418 --out plink_trial

just to see as to how the following command gives the output as I am using plink for the first time , it however gives me the following error

ERROR: Could not place marker for left window edge even when there is a SNP present at 3721318

[zx8754]

Relevant post: What Does The Plink Error: "Could Not Place Marker For Left Window Edge" Mean?

[Aishwarya.Kulkarni]

Saw that but did not get a concrete answer rom the post.

Answer 1

[Philipp Bayer]

Have you tried subtracting a bit more in the --from-bp part, i.e., 3721118, 3721018 etc., it looks to me like there's just not enough SNPs in that window between 3721218 and 3721418.

[Aishwarya.Kulkarni]

Hi Philipp, shall try that and see.

[Aishwarya.Kulkarni]

Tried adding larger window, still not working. :(

Answer 2

[Aishwarya.Kulkarni]

Also I issued the command

plink --noweb --bfile hapmap1 --recode --filter-controls --snp rs2887274 --window 100 --out plink_trial2

and it gave the results inspite of trying for same region in from ,to parameters.

[Philipp Bayer]

How many SNPs did that one result in? Just one? The manual says:

Alternatively, you can specify a single SNP and, optionally, also ask for all SNPs in the surrounding region,

So I'd assume that you got only one SNP. Looking at PLINK's code that generates the 'Could not place marker for left window edge', it looks like it's trying to extract at least two SNPs, one for the left edge, and one for the right edge.