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Count number of SNPs per chromosome in vcf file

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
• 8,043 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by mostafarafiepour mostafarafiepour

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
• 1 views • link
written by cpad0112 cpad0112

I have adapted your title to make it more descriptive of what you are asking.

• 1 views • link
written by WouterDeCoster WouterDeCoster

1 answer

UPDATE 2021: if your VCF is indexed: bcftools index -s indexed.vcf.gz

grep -v "^#" in.vcf | cut -f 1 | sort | uniq -c
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

many thanks for your reply,

Does -f 1 mean the number of chromosomes?

• 1 views • link
written by mostafarafiepour mostafarafiepour

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.

• 1 views • link
written by Kevin Blighe Kevin Blighe

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

• 1 views • link
written by mostafarafiepour mostafarafiepour

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

Upvote|Bookmark|Accept

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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.

• 1 views • link
written by mostafarafiepour mostafarafiepour

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

• 1 views • link
written by cpad0112 cpad0112

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