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SNP,INDEL counting per chromosomes in vcf

Hi all, how can I counting SNPs and INDELs per each chromosome in a vcf file?

snp next-gen snp vcf
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updated by Alex Reynolds Alex Reynolds • written by Siavash Salek Ardestani • Siavash Salek Ardestani

2 answers

Using BEDOPS vcf2bed and standard Unix tools like wc to count lines:

$ vcf2bed --snvs < variants.vcf | wc -l
$ vcf2bed --insertions < variants.vcf | wc -l
$ vcf2bed --deletions < variants.vcf | wc -l

Cf. http://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/vcf2bed.html

The above does counts over all chromosomes. You need to do an extra step to count per chromosome.

To perform this count exercise quickly per-chromosome, per-variant class:

$ vcf2bed --snvs < variants.vcf > variants.snvs.bed
$ for chr in `bedextract --list-chr variants.snvs.bed`; do echo $chr; bedextract $chr variants.snvs.bed | wc -l; done

The bedextract tool is part of BEDOPS. If you install BEDOPS to get vcf2bed, you get bedextract, as well.

Repeat this procedure for --insertions and --deletions, replacing snvs accordingly, to count those classes.

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written by Alex Reynolds Alex Reynolds

I run these commands and I have number of SNP per chromosomes furthermore I have many 'Un' (I think this is unknown chromosomes SNP). how can I split or cut mt,x and unknown chromosomes from vcf?

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written by Siavash Salek Ardestani • Siavash Salek Ardestani

Use grep on the output of bedextract --list-chr. You can pass grep a file containing chromosome names you want to include (or, conversely, exclude) via grep -f. 

$ for chr in `bedextract --list-chr variants.snvs.bed | grep -f wanted-chromosomes.txt -`; do ... ; done

Run man grep to see a full list of options.

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written by Alex Reynolds Alex Reynolds

many thanks but I want cut mt, unknown and X chromosomes SNPs from a vcf file.

I means, my prior vcf have many SNPs that these SNPs are in mitochondrial DNA, X chromosome and unknown chromosomes. I want to have a vcf file without mitochondrial , X chromosome and unknown chromosomes SNPs information.

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written by Siavash Salek Ardestani • Siavash Salek Ardestani

You could use grep in the same way. It may help to review some examples of how it works so you can understand Unix streams and how grep can be used here.

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written by Alex Reynolds Alex Reynolds

Hi, I also tried using this script but gave me only the number of snvs for each chromosome and did not count the insertions and deletions??

In fact, the outputs related to insertions and deletions are empty and there is no data in it?

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written by mostafarafiepour mostafarafiepour

Are you sure you have insertions/deletions?

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written by Ram Ram

yes, Because when I use this command, i find 182456 deletions and 0 insertions.

insertions:

awk '! /\#/' variants.vcf | awk '{if(length($5) > 1) print}' | wc -l

insertions:

awk '! /\#/' variants.vcf | awk '{if(length($4) > 1 ) print}' | wc -l
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written by mostafarafiepour mostafarafiepour

using bioalcidaejdk: http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

$ java -jar dist/bioalcidaejdk.jar -e 'stream().map(V->V.getType().name()+" "+V.getContig()).collect(Collectors.groupingBy(Function.identity(), Collectors.counting())).forEach((K,V)->{println(K+" : "+V);});'  input.vcf

SNP 1 : 44
INDEL 1 : 6
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written by Pierre Lindenbaum Pierre Lindenbaum

Hi, i have been trying to do your scripts. But counted the only number of SNPs and did not count the InDels. ? Please see the photo in the attachment.

enter image description here

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written by mostafarafiepour mostafarafiepour

Read the part that begins with [WARN]

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written by Ram Ram

Ah I see. It's probably my second guess then - no InDels to pick.

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written by Ram Ram

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