Low frequency indel detection

[NestorNotabilis]

Hi,
Can anyone recommend software particularly suited for very low frequency indel detection as might be applied to ultra-deep targeted sequencing (UDT-seq) datasets where coverage exceeds 1000x? Choices seem limited. Am getting the impression scripting around samtools mpileup output might be the most robust strategy. Any thoughts anyone?

Many thanks.

[Artem]

I am also interested in indel annotation, if you find any good solutions please post.

[bioinfosm]

I agree .. you would need to parse the pileup file and then use your own thresholds. Perhaps use the simple common filters and start with that indel list.

For annotation, seattleSEQ (http://snp.gs.washington.edu/SeattleSeqAnnotation/) is an option and so is TREAT (shameless self plug - http://www.ncbi.nlm.nih.gov/pubmed/22088845)

[bioinfosm]

Hi,
Can anyone recommend software particularly suited for very low frequency indel detection as might be applied to ultra-deep targeted sequencing (UDT-seq) datasets where coverage exceeds 1000x? Choices seem limited. Am getting the impression scripting around samtools mpileup output might be the most robust strategy. Any thoughts anyone?

Many thanks.

ohh well, here is another option, though am not sure if variants includes indels

http://seqanswers.com/forums/showthread.php?t=18541