best tool for indels?

[vasvale]

hello

we have a sample with a 10 bases deletion and 2 nt insertion that is not detected with the following tools: eland-extended+Casava/bwa-gatk/bfast

any suggestion on what else to try?

thanks

Vasvale

[bioinfosm]

thats strange. Do you know why it is missed using those tools? Any others that were expected and found?

Maybe you need to look at visualization of mapped reads in that region (using IGV or similar) to get an idea of whats going on. Is there even read coverage in that region..

[lh3]

You may try stampy/novoalign+dindel. If that fails, your indels are intrinsically unable to be called.

[krobison]

I'd break the question into two parts -- (1) are you seeing alignments of reads bearing the variant (2) are those reads leading to an indel call.

Obviously if #1 fails then #2 can't possibly work.

[Torst]

we have a sample with a 10 bases deletion and 2 nt insertion that is not detected with the following tools: eland-extended+Casava/bwa-gatk/bfast

To give some context, could you let us know the size/nature of the reference genome, and the technology/readlength/yield of the reads?