Question: Transition/Transversion Ratio From Fastq Files
3
gravatar for venkateshr89
5.9 years ago by
venkateshr89690
United States
venkateshr89690 wrote:

Hi,

I was doing QC for my paired-end exome data which is in FASTQ format. I used FASTQC for the QC but I am more interested in looking at the Transition/Transversion ratio. Is there any tool that can give us the transition/transition ratio?

Thanks

ADD COMMENTlink modified 5.7 years ago by rob234king570 • written 5.9 years ago by venkateshr89690
4

Don't you need to compare similar sequences (then assumed as homologous) to derive substitution type estimates?

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Manu Prestat3.9k
1

I am very confused, fastq gives you raw sequences. to get transition/transversions, you need aligned reads to a reference.

ADD REPLYlink written 5.9 years ago by Gabriel R.2.6k
3
gravatar for Chris Miller
5.9 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

You're several steps short of looking at Ti/Tv ratios. I'm going to talk about this in the context of cancer, because it's what I'm most familiar with. Your steps will be something like:

  • use an aligner (like BWA) to align both your tumor reads and normal reads to the reference genome.
  • Use a variant caller (samtools, Varscan, strelka, etc) to identify somatic snvs
  • determine whether each of these sites was a transition or transversion, then calculate the rates.
ADD COMMENTlink written 5.9 years ago by Chris Miller20k
2

Thanks Chris. So which tool you think can be used to calculate the ti/tv rate?

ADD REPLYlink written 5.9 years ago by venkateshr89690
1

Once you get your list of mutations, it will contain the reference and variant bases for each. With that information it's very straightforward to write a script that counts whether each is a transition or transversion. http://www.mun.ca/biology/scarr/Transitions_vs_Transversions.html

ADD REPLYlink written 5.9 years ago by Chris Miller20k
1

Perfect. Thanks :)

ADD REPLYlink written 5.9 years ago by venkateshr89690

Once you have a vcf produced by a variant caller you can run GATK VariantEval: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_varianteval_VariantEval.html

It will produce statistics on your variant, including Ti/Tv ratio.

ADD REPLYlink written 5.7 years ago by William4.4k
2
gravatar for zam.iqbal.genome
5.9 years ago by
United Kingdom
zam.iqbal.genome1.7k wrote:

Also, you may know this, but worth saying, Ts/Tv varies between species (not sure what species you are using).

ADD COMMENTlink written 5.9 years ago by zam.iqbal.genome1.7k
2

I am using Human sequence data

ADD REPLYlink written 5.9 years ago by venkateshr89690
1
gravatar for rob234king
5.7 years ago by
rob234king570
UK/Harpenden/Rothamsted Research
rob234king570 wrote:

If you have vcf file to annotate use snpEff and in the html report it will show amongst other things the ratio you want.

ADD COMMENTlink written 5.7 years ago by rob234king570
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