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Detection nucleotide changes in VCF file

Hi,

I have a small question. I just started to work with bash and i want to count the amount of specific mutations my file has.

So for example; A >>> T

Not al the mutations but just one mutation on its own, compared to the reference genome.

The file I use is an VCF-file

Thank you in advance!

mutation linux vcl next-gen alignment
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by stan.aanhane • stan.aanhane

1 answer 

bcftools view --no-header -i 'REF=="A" && ALT=="T" ' input.vcf | wc -l

or using awk

awk -F '\t'  '($4=="A" && $5=="T" && !($0 ~ /^#/))' input.vcf | wc -l
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written by Pierre Lindenbaum Pierre Lindenbaum

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Upvote|Bookmark|Accept

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written by Ram Ram

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