Count number of SNPs per chromosome in vcf file
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2.6 years ago

Hi all,

I want to count the number of SNP for each chromosome in the raw VCF file. What is the best idea?

Best Regard

Mostafa

SNP • 3.0k views
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Normalize your VCF and then execute: Datamash is in most of the linux repos

$ grep -v '^#' test.vcf | datamash -sg 1 count 1

with awk:

$ awk '!/^#/ { a[$1]++ } END {for (i in a) print i,a[i]}' test.vcf
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I have adapted your title to make it more descriptive of what you are asking.

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2.6 years ago
grep -v "^#" in.vcf | cut -f 1 | sort | uniq -c
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many thanks for your reply,

Does -f 1 mean the number of chromosomes?

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I apologize but this script does not work?

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Pierre's script works for me, Moustafa:

grep -v "^#" test.vcf | cut -f 1 | sort | uniq -c
  16011 1
   7308 10
   9565 11
   9149 12
   3311 13
   5881 14
   5360 15
   7016 16
   8611 17
   2896 18
   9895 19
  11621 2
   3881 20
   2472 21
   3881 22
   9215 3
   7464 4
   7805 5
  10110 6
   7991 7
   6023 8
   6898 9
     37 MT
   3218 X
     21 Y

Chromosome 1 has 16011 variants... chromosome 9 has 6898, et cetera.

Your input VCF should be properly formatted and also be uncompressed.

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Yes i understood. Thank you very much for describing you.

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If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Upvote|Bookmark|Accept

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Now, if i want to count the number of SNPs for each Breed, what is the best idea? i have 5 breed in the my raw vcf.

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try VCFstats from RTGtools. But that would be stats per sample, not per chromosome. If you want per chromosome, per sample, then you may have to write a script. mostafarafiepour

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