Phaseme is running in precomputed mode. The input VCF file at 39219.vcf is empty or does not exist or the first column (showing the chromosomes) is not a sole number (It shouldn't be chr1!) or you are not running PhaseME on Linux

[wangjie07070910]

Many thanks for providing this tool. I'm having trouble using this tool. I tried to use it to analyze one of my phased vcf files that contain one sample of one chromosome and my code is as follows：

python phaseme.py quality39219.vcf out_39219

Then, I got the error:
Phaseme is running in precomputed mode. The input VCF file at 39219.vcf is empty or does not exist or the first column (showing the chromosomes) is not a sole number (It shouldn't be chr1!) or you are not running PhaseME on Linux

I did run it on linux. The first column of my vcf file contains only one chromosome and its name is 39219

The image is a screenshot of my vcf file

[sinamajidian]

Dear @wangjie07070910
Thanks for using our tool. PhaseME is based on the population phasing information extracted from 1000 human genomes (1kGP) which cover chromosomes 1 to 22 of human reference genome. Unfortunately, the current version of PhaseME solely work on chr 1-22. I guess your case is not human or it includes some scaffold as you mentioned the chromosome name is 39219.

For the nonhuman case, if we have phasing of several individuals, we can train phasme (extract pairs) to improve phasing of another non-human species.
If it is human and scaffolds, we could try to use a lift-over method to have a new vcf based on human reference genome or a kind of whole-genome mapping.
I hope it helps.
And sorry for inconvenience, I should have clarified this issue in the readme.
Regards, Sina