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grenaud / glactools

command-line tools for the management of genotype likelihoods and allele counts
http://grenaud.github.io/glactools/
GNU General Public License v3.0
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Error in vcfm2acf #29

Closed LiShuhang-gif closed 2 years ago

LiShuhang-gif commented 2 years ago

Hi, I am currently trying to convert a VCF file to an ACF file using glactools. However, I have encountered the following error message:

Error, missing data in the EPO file
Error: GlacParser tried to read 4 bytes but got 0

I tried the solution in another issue. I've rewritten "chr22" as "22". However, this allowed some chromosomes to run smoothly, while others still reported errors. 

Error, missing data in the EPO file
Warning: No EOF marker, likely due to an I/O error
Error: GlacParser tried to read 2 bytes but got 0

I wonder if you have any suggestions for this? By the way, my variants were mapped to hg38 rather than hg19/37. Could this be the cause of the error message? Looking forward to your reply, thank you!

grenaud commented 2 years ago

Hello! Yes the EPO was computed on hg19 not 38. I will write on my to-do list to try to find an EPO alignment that for hg38. Thank you for bringing this my attention.

LiShuhang-gif commented 2 years ago

Thank you for your reply! I am looking forward to your newly generated EPO file on hg38. By the way, I would like to ask how to obtain the required outgroup EPO file? Is it calculated by any software? Or which website can I download it from? Thanks!

grenaud commented 2 years ago

Yes I parse them using https://github.com/grenaud/epoParser feel free to have a go at it if you want :-) The EPO for hg38 seems to be available here:http://www.ensembl.org/info/genome/compara/mlss.html?mlss=1993

LiShuhang-gif commented 2 years ago

Thanks again! I want to make sure whether the EPO files of chimpanzee downloaded from this website can directly be used in glactools? Or should I parse the EPO file of chimpanzee which I download from this ensembl website using epoParser first?

grenaud commented 2 years ago

Not directly, you need to run it through epoParser which will produce a tab-delimited file.

LiShuhang-gif commented 2 years ago

Hi, I'm really sorry for the late reply due to my busy assessment. By the way, I was wondering if you generated an EPO file for hG38? Thanks!

grenaud commented 2 years ago

Hey! I manage to find the EPO files on the ensemble FTP, I am parsing it now. Buzz me again next week.

LiShuhang-gif commented 2 years ago

Hey! I wonder if you have already found the EPO files on the ensemble FTP and generated an EPO file for hG38? Thanks in advance!

grenaud commented 2 years ago

Yes! The files are here now:

ftp://ftp.healthtech.dtu.dk/public/EPO/all_hg19.epo.gz ftp://ftp.healthtech.dtu.dk/public/EPO/all_hg19.epo.gz.tbi ftp://ftp.healthtech.dtu.dk/public/EPO/all_hg38.epo.gz ftp://ftp.healthtech.dtu.dk/public/EPO/all_hg38.epo.gz.tbi

My apologies for the delay! I've also uploaded a new README with these links.

Let me know if you run into any trouble