Finding Indel's and long inversions in GA data

[apratap]

Hi All

I am looking for tools to find indel in GA data (short and long) and also look for large inversions after de novo assembly and comparing to reference genome.

In the past I have used VarScan and samtools for finding indel but just wondering if people are using other software for finding indels and ways in which large inversion could be detected.


PS: I have looked at the software wiki but would like to try tools based on your experience.

Thanks!
-Abhi

[colindaven]

Hi,

We haven't got into this massively as we only have 36 bp single end reads from bacteria.
However initial results have been disappointing. We used Shrimp1 for alignment and attempted to verify 3 small <5bp indels in the wetlab. All failed, despite having 10+ reads predicting their presence.

We tried to verify another 8 by Sanger sequencing. It turns out the sequencing was poor, and these are associated with tricky repeat rich bacterial regions.

It seems the aligners are having some trouble with indels.

What has your experience been like ?

[apratap]

Hey Collindaven

Thanks for sharing your insight. I unfortunately work only on the informatics side only and till now haven't heard back from the team for whom we did the insilico indel analysis in the past. So I dont know the false positive rate.

What I hear and read from papers that people are finding it more useful to do indel analysis with paired end data as it gives more room to find long indels based on the known evidence of the expected distance where the read 1/2 should map.

Thanks!
-Abhi

[apratap]

Hey Guys

Just pushing this once more. I would appreciate if you could share some insight on finding long/short indel in GA data and also detecting long inversions.

Thanks
-Abhi