VCF header line counting
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Hello happy bioinformaticians :)
It can be a very simple question but I want to ask that how can I count line (row) of header of VCF ?
I can be done manually but I want to get accurate result.
Simply count the number of rows starting with a
grep -c '^#' <vcf>
If you want to count the number of sequence headers:
grep -c '##contig' <vcf>
And even more.. if you want to count the number of non-headers:
grep -c '^[^#]' <vcf>
On the command line of course ;)
updated 13 months ago by
written 8.3 years ago by
I think this would be the fastest
bcftools view --header-only <vcf> | wc -l
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The grep command will read the entire file, so if your VCF file is very large, something like this will run faster:
Thanks it was so helpful !!!
Thanks !! :)
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