[Vcftools-help] issues with vcftools when using multiple chromosomes

[Madleina C. <mad...@un...>]

Hi,

I'm trying to convert a vcf-file to a BEAGLE file using vcftools. 
Because my data comes from a non-model organism, the reference genome I 
have is really bad and my vcf-file contains about 5'000 "chromosomes" 
(which are not actually chromosomes, but rather pieces of chromosomes).

The command I use is (for one chromosome):

vcftools --gzvcf new.vcf.gz --out  output_beagle --BEAGLE-GL --chr 
NC_015762.1

This works fine. However, I want to dump all my chromosomes (which are 
around 5'000) into the same BEAGLE file. First, I tried doing something like

vcftools --gzvcf new.vcf.gz --out  output_beagle --BEAGLE-GL --chr 
NC_015762.1 --chr NC_015763.1

where I used the flag --chr several times with different chromosome 
names. However, this throws an error

"Error: Require a chromosome (--chr) when outputting Beagle likelihoods."

I also tried

vcftools --gzvcf new.vcf.gz --out  output_beagle --BEAGLE-GL --chr 
NC_015762.1,NC_015763.1

where I separated my chromosomes by commas, but this also didn't work, 
and returned the somewhat weird error message

"Error: Require GL or PL FORMAT tags in VCF file to output BEAGLE input."

I'm confused because the man-pages say about --chr that "these options 
may be used multiple times to include or exclude more than one 
chromosome", so I expected the first option to work.

But actually, it would also be really nice if I could either just omit 
the --chr, such that it would use all chromosomes by default; or if I 
could give the name of a file where all my chromosome names are listed 
(because typing --chr X --chr Y --chr Z etc. is a bit annoying for 5000 
chromosomes)...

I'm using VCFtools version 0.1.17.

Can you tell me if I do something wrong? In case you need my vcf-file, 
please let me know.

Thanks a lot in advance! Best,

Madleina