Reporting alleles sequences for Amplicon sequencing after variant calling

Question

[Aurelie MLB]

Hello,

I have amplicon sequencing data for clones whose genome has been edited. On each alleles, there might be one or two indels. I would like report the sequences of the alleles and their frequency. I have some complex cases where some clones are mixed clones. May I ask if there is an obvious tool to work out what are the amplicon sequences from a variant caller result or do I have to look at all the reads and work out which variants are combined in one sequence?

[Kirill Tsyganov]

@Aurelie MLB I might have very similar problem if not the same. I'm also seeking solution for that. We can kinder of help each other by sharing info. Although this isn't a discussion forum as such, but if we can provide a solution or at least point people in the right direction I think It will super useful to other biologist and bioinformaticians.

Have a look at this tool https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php

Also you might need to clarify/explain you question a bit better to me because I'm not exactly sure what you are trying to do...

Here is what I have got: a mouse that had short sequence mutation introduces (~ 26 bp I think (i didn't do the experiment)) Mouse had been sequenced, targeting sequence to the region of the mutation. I can see InDels and other SNP's in IGV. I need reliable method to confidently call and InDel. The problem is not all reads will have a mutation..

I tried that method about and also samtools mpileup and bcftools. I'm still looking for the solution

Cheers

[Aurelie MLB]

Hi,

What you want is a variant caller I think. You could check gatk, freebayes, gatk-haplotype, platypus, mutect, scalpel, vardict, varscan, samtools... If you want a tool specifically designed for indels, you could have a look at scalpel, pindel, sid...

My question was a bit different I think as I wanted to find the existing combinations of variants for a short region (to identify the sequence of all alleles). This a step further after variant calling. I did not find an already existing tool doing this really unfortunately.