Thanks for your answer, I'll just want to know if I missed something like 'bcftools list-contigs'
Le 18/09/2018 à 14:08, Braulio Valdebenito Maturana a écrit :
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. _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
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