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Question: VCF header line counting
1
gravatar for basalganglia
5.9 years ago by
basalganglia • 40
England
basalganglia • 40 wrote:

Hello happy bioinformaticians :)

It can be a very simple quesion 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
header vcf • 4.3k views
ADD COMMENT • link •
modified 5.9 years ago by Biostar ♦♦ 20 • written 5.9 years ago by basalganglia • 40

Thanks !! :)

ADD REPLY • link written 5.9 years ago by basalganglia • 40

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

ADD REPLY • link written 5.9 years ago by _r_am ♦ 32k
9
gravatar for Coryza
5.9 years ago by
Coryza • 390
Netherlands
Coryza • 390 wrote:

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 ofcourse ;)
ADD COMMENT • link modified 5.9 years ago • written 5.9 years ago by Coryza • 390
5

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

 

 

ADD REPLY • link written 5.9 years ago by Len Trigg • 1.5k

Thanks it was so helpful !!! 

ADD REPLY • link written 5.9 years ago by basalganglia • 40
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