Dear Sebastien,
what’s wrong with the command? It seems to work well. Only thing is you’ll need
to parse the result to remove the lengths.
Best regards,
Braulio.
El 18-09-2018, a las 5:16, sebastien letort <sebastien.let...@irisa.fr>
escribió:
> Hi,
>
> In order to do some parallelization, i wanted to get the list of chromosomes
> from my bcf file, but I couldn't find a command to do that.
>
> My only guess is :
>
> bcftools view -h my_file.bcf | perl -lne 'if( /^##contig=<ID=(.+)>/ ){ print
> $1; }'
>
> any better solution ?
>
> Sébastien L.
>
>
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