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odelaneau / GLIMPSE

Low Coverage Calling of Genotypes
MIT License
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GLIMPSE2_ligate: Three files overlapping at position #196

Open Truongphikt opened 8 months ago

Truongphikt commented 8 months ago

Hi, after I run GLIMPSE2_phase to impute chunks then use GLIMPSE2_ligate to stick them together. Unfortunately, I run into a bug: image

I have three chunks that overlap each other. As I checked, it's exactly what I thought, three vcf files are overlapped at the 27804801 position:

  NA20359_22_25016859_27816902.bcf
  NA20359_22_27016901_31930215.bcf
  NA20359_22_27804801_33263344.bcf

image

My question is: What are the frequent reasons that cause overlapping phenomena?

Thank you.

This is my log file: .command.log

==== Update

drneavin commented 4 months ago

I've run into the same issue with chromosomes 1 and 22. It appears to be at a slightly different location on chromosome 22 for my files:

ERROR: Three files overlapping at position: 27813503

All other chromsomes are fine and can be easily ligated. I've regenerated the chunks and imputation with the same result.

I'm wondering if you were able to resolve this @Truongphikt ?

Truongphikt commented 4 months ago

@drneavin I passed this error by increasing the --window-mb parameter (default is 4) at the chunking step.

drneavin commented 4 months ago

Thank you! This resolved my issue when I set it to 6 (didn't try any other values)

sandra-selfdecode commented 2 months ago

I noticed that I had almost twice as many chunks after updating from the 2.0.0 release to 2.0.1, and then I got the same error in the ligate step. Looking back at my log for the chunking step, it says * Min. Window size : [2.5cM | 2Mb | 20000 variants], and I used the default parameters. I think the defaults listed in the documentation might refer to 2.0.0.

PMuchina commented 2 months ago

I overcame this issue by changing the --window-mb to 4. The default was 2.