vcfm2acf issue about glactools HOT 7 OPEN

Could you check the ALT field? ? do you have a * in there?

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Thanks for your comment.
I have solved the aforementioned issues.

However, I had another issue in using EPO file.

The command line was as followed:
glactools/glactools vcfm2acf --onlyGT --epo all.epo.gz --fai human_g1k_v37.fasta.fai test > test.acf.gz

Then the error message was as followed:
Error, missing data in the EPO file

I wonder if you have any clue what this error message means?

Thanks for your help in advance.

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Is it possible that there is a different encoding of chromosomes? "1" vs "chr1"

from glactools.

Great!
Removing 'chr' from my VCF file helps and ACF file seems to be made partially.
(Previously, ACF file was not made at all.)
However, the error message pops out after a while.
Could you suggest any other reason for this message?

Thanks in advance.

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just to be sure, are you sure your variants were mapped to hg19/v37? Are there chromosomes that are not 1,2,3..22? did you remove any _random chr? can you do a cut -f 1 |uniq -c on column 1?

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Hello I got an issue
I run vcfm2acf with a merged of multiple vcf files generated by haplotype caller in GATK. and my reference genome was at the scaffold level.

my command:
./glactools vcfm2acf --onlyGT --fai ReferenceGenome.fasta.fai my.vcf > my.acf

but I got this error:
the PL does not have 3,6, or 10 fields, has 1 fields

Does anyone know how to fix this problem?

Best,
BAGUS

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Can you please post a few of the lines that are causing the problem?

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