ERROR: Overlap between buffer-specific variants

[drneavin]

Hello,

I'm very excited to be using GLIMPSE for imputation/phasing of low coverage variants called from sequencing data. However, I've started to run into this error for the ligate step:

ERROR: Overlap between buffer-specific variants

Which I have seen in other issues is sometimes related to indels but in my case there are no indels in my files. I'm running glimpse v1.1.1 from the pre-computed binaries. There were no errors from the GLIMPSE_phase_static. Further, I'm running ligate on each chromosome separately for multiple different samples and it seems to work for some chromosomes of some of the samples but not others. Any thoughts on how I can resolve this would be fantastic! Please let me know if you require any additional information or details to help identify the issue.

Update

I think that this issue is coming from SNPs that are called as non-buffer SNPs in one chunk (BUF=0) but are showing up as buffer SNPs in the another chunk. For example, this SNP is annotated as a buffer SNP in chunk 9:

chr21   32748819        rs1021057312    G       A       .       .       RAF=0.000450315;AF=0;INFO=1;BUF=1      GT:DS:GP:HS     0/0:0:1,0,0:0

but in chunk 10 this is a non-buffer SNP:

chr21   32748819        rs1021057312    G       A       .       .       RAF=0.000450315;AF=0;INFO=1;BUF=0       GT:DS:GP:HS     0/0:0:1,0,0:0

But I'm still at a loss for how to resolve this since it seems to be happening for most of the chromosomes for most of my samples.

Thanks for the help,
Drew

[drneavin]

An update for anyone else who ends up here. I used some map files that I had used for another project but had forgotten to update the chromsome encoding (chr1, chr2, chr3 vs 1, 2, 3). What's strange is that glimpse phasing ran without a problem and some of the chromosomes were able able to ligate while others couldn't. Updating the map file and rerunning resolved the issue. Still leaving this open since I think this should be built in as an error when running glimpse phase