VCF header line counting
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9.6 years ago
basalganglia ▴ 40

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.

Thanks,
BG

vcf header • 7.8k views
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10
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9.6 years ago
Coryza ▴ 430

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 ;)

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5
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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:

sed -n '/^[^#]/q;p' <vcf> | wc -l
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Thanks it was so helpful !!!

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Thanks !! :)

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Please accept Coryza's answer if it was helpful, otherwise give them feedback on why it did not address your problem.

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16 months ago
beausoleilmo ▴ 590

I think this would be the fastest

bcftools view --header-only <vcf> | wc -l
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