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
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
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:
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
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.
Also, you may know this, but worth saying, Ts/Tv varies between species (not sure what species you are using).
If you have vcf file to annotate use snpEff and in the html report it will show amongst other things the ratio you want.
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Don't you need to compare similar sequences (then assumed as homologous) to derive substitution type estimates?
I am very confused, fastq gives you raw sequences. to get transition/transversions, you need aligned reads to a reference.