Hi,
best is to use the csi index (provided the file is indexed):
bcftools index -s file.bcf
The command also prints the chromosome lengths and the number of
records
Petr
On Tue, 2018-09-18 at 10:16 +0200, sebastien letort wrote:
> 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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