Question: Finding distribution of indels from vcf file
1
gravatar for ApoorvaB
2.5 years ago by
ApoorvaB190
United States
ApoorvaB190 wrote:

I have a vcf file from a single cell experiment. I got the basic statistics using vcf-stat utility in vcf-tools. I am interested in the distribution of indels. How can i get a barplot of genome-wide indel distribution (number of indels per chromosome) as well as a plot of number of insertions/deletions versus size of insertion/deletion? Is there a tool that I can use ?

barplots samtools vcf • 1.2k views
ADD COMMENTlink modified 2.5 years ago by Brice Sarver2.5k • written 2.5 years ago by ApoorvaB190
3
gravatar for Brice Sarver
2.5 years ago by
Brice Sarver2.5k
United States
Brice Sarver2.5k wrote:

The VCF will have all of this information. One way to summarize all of your data would be to use grep to thin your VCF down to just indels, then read the (tab delimited) result into R and plot whatever you want. Note that, per record, you'll have a chromosome, start position, and stop position, which should give you everything you'll need. Other tools might be able to handle this, but it's just basic text parsing to get what you want.

ADD COMMENTlink written 2.5 years ago by Brice Sarver2.5k

That helped. thanks !

ADD REPLYlink written 2.5 years ago by ApoorvaB190
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