This is a test version of Biostars. For the public version, visit https://www.biostars.org.
VCF header line counting

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
• 9,214 views • link
updated by beausoleilmo beausoleilmo • written by basalganglia • basalganglia

2 answers

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 ;)

• 1 views • link
updated by Ram Ram • written by Coryza Coryza

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

• 0 views • link
written by Ram Ram

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
• 0 views • link
updated by Ram Ram • written by Len Trigg Len Trigg

I think this would be the fastest

bcftools view --header-only <vcf> | wc -l
• 0 views • link
written by beausoleilmo beausoleilmo

Log in to answer this question.

More posts like this