Running Pindel prior to Dindel

[keesa]

Hi Jason,

the current version of Dindel does not do a banded alignment of reads against haplotypes. As a result, very long haplotypes will become memory and time-intensive to analyze.

For the 1000 Genomes project I considered candidate indels up to 50 bp. Dindel will make sure that the haplotype is long enough to contain the variant in the case of a deletion. Currently, Dindel will only consider variants that can be expressed as an insertion or a deletion, so this makes it not particularly suited to genotype or call SVs in general.

I am working on a version that takes any VCF4 variant (any REF, ALT combination) sequence as input, and will perform the alignment more efficiently so that longer (>50 bp) variants can be handled as well.

Kees

[KaiYe]

hi Jason,

I should work on a script to convert Pindel output for VCF 4.0 as it is requested by the members of 1000 genomes project. I need to find time for it.

In Dindel paper, the simulated indels are 1-10bp and they are short insertions and deletions. Could Kees comment here? What is the maximum size of indel you would recommend users to push into Dindel?

To my knowledge, inversions, non-template sequence and tandem duplications are better characterized as structural variants (SV). Could Kees indicate whether SVs will be handled by Dindel?

I would position Pindel as primary variant caller. It doesn't report genotyping likelihood yet. If Dindel could cover genotyping of both short indels and SVs, I would rather do something else more useful to the community.

Kai

[jtjli]

In the Dindel manual, it recommends generating candidate indels using Pindel.

Has any one got experience with that?

I'm trying to achieve that but have the following questions:
1) Pindel generates 6 files for each chromosome. Can we potentially convert all of them as candidate indels for Dindel? Or
2) is there a limit on the size of indel that can be processed by Dindel (120bp?)?
3) Is there a restriction on the type of indels that can be processed by Dindel, e.g. will it handle inversion, non-template sequence insertion+deletion?
4) Does anyone have scripts to share for converting Pindel output to a format that can be handled by Dindel?

Thanks
Jason
jason.li @ petermac.org