Question

Count all variants from vcf file

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2.3 years ago

t.ali • 0

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 • 947 views

ADD COMMENT • link updated 7 months ago by Pierre Lindenbaum 164k • written 2.3 years ago by t.ali • 0

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zgrep -cv "^#" <vcf_file>

ADD REPLY • link 2.3 years ago by Arup Ghosh 3.2k

score 1 · Answer 1 · 2022-08-25

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2.3 years ago

raphael.B ▴ 520

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

ADD COMMENT • link 2.3 years ago by raphael.B ▴ 520

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I tried this and it worked. Thanks alot

ADD REPLY • link 2.3 years ago by t.ali • 0

score 1 · Answer 2 · 2022-08-25

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2.3 years ago

Pierre Lindenbaum 164k

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

ADD COMMENT • link 7 months ago by Pierre Lindenbaum 164k