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Count all variants from vcf file

I have vcf files from gatk pipleline, now I want to count all the variants in a file. Can anyone help? Thanks

variants vcf count
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by t.ali • t.ali 
zgrep -cv "^#" <vcf_file>
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written by Arup Ghosh Arup Ghosh

2 answers

Hello! You can use bcftools query -f "A\n" <your_vcf> | wc -l

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written by raphael.B • raphael.B

I tried this and it worked. Thanks alot

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written by t.ali • t.ali 
bcftools query -N -f '.' in.vcf | wc -c

or

  bcftools index -s indexed.vcf.gz |  cut -f 3 |  paste -s -d '+' | bc

EDIT 2024: there is now a new behavior in bcftools query:

    -N, --disable-automatic-newline   Disable automatic addition of newline character when not present
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written by Pierre Lindenbaum Pierre Lindenbaum

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