Question: SNP,INDEL counting per chromosomes in vcf
1
gravatar for siyavash_damdar
18 months ago by
siyavash_damdar20 wrote:

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

snp next-gen vcf • 1.4k views
ADD COMMENTlink modified 18 months ago by Alex Reynolds28k • written 18 months ago by siyavash_damdar20
2
gravatar for Alex Reynolds
18 months ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

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.

ADD COMMENTlink modified 18 months ago • written 18 months ago by Alex Reynolds28k

it is correct. I humbly thank you,

ADD REPLYlink modified 18 months ago • written 18 months ago by siyavash_damdar20

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?

ADD REPLYlink written 18 months ago by siyavash_damdar20

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.

ADD REPLYlink written 18 months ago by Alex Reynolds28k

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.

ADD REPLYlink written 18 months ago by siyavash_damdar20

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.

ADD REPLYlink written 18 months ago by Alex Reynolds28k

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?

ADD REPLYlink written 10 months ago by mostafarafiepour60

Are you sure you have insertions/deletions?

ADD REPLYlink written 10 months ago by RamRS22k

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
ADD REPLYlink modified 10 months ago • written 10 months ago by mostafarafiepour60
0
gravatar for Pierre Lindenbaum
18 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

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
ADD COMMENTlink written 18 months ago by Pierre Lindenbaum121k

thanks but Did not respond

ADD REPLYlink written 18 months ago by siyavash_damdar20

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

ADD REPLYlink modified 10 months ago • written 10 months ago by mostafarafiepour60

Read the part that begins with [WARN]

ADD REPLYlink written 10 months ago by RamRS22k

the warning is meaningless here.

ADD REPLYlink written 10 months ago by Pierre Lindenbaum121k

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

ADD REPLYlink written 10 months ago by RamRS22k
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