[mathieu]

lh3: I will try BAQ right away to see if it improves things. Thanks for the advices

[mathieu]

Apparently BAQ is only applicable to base sequences and not yet for color (solid) sequence yet.

[lh3]

BAQ does not work well for solid (reduced power), but it works.

[Michael.James.Clark]

Yeah, what I'm trying now and which seems to give very nice numbers of variants and ts/tv ratio is align->GATK realign/recalibrate(cleans up alignments)->BAQ->GATK Unified Genotyper(Dindel for indels). GATK's built-in filters are very nicely calibrated, at least in human.

Actually, Dindel is reporting more indels than I expect (a little under twice as many), but it could be that it's significantly more sensitive than samtools. But that's another thread.

[Tim Hague]

Hi epigen & John,
Thanks for your advices. I tried to install bioscope on our cluster but I gave up... Concerning BWA, it is the first one I tried and I was quite disappointed by the results since it has been highly recommended with low mapping rate (22.6%). The first results I have using BFAST and ShRIMP are almost the same in term mapping rate (57.5% and 51.2% respectively). However ShRIMP was a bit faster.

@epigen: For the SNP et InDels calling I am using samtools so far, but I am not very satisfied there are too many miscalls. What are your advices?

If you're looking for aligners that find indels you could try the Omixon Variant Toolkit. It's a gapped aligner with spaced seeds similar to ShRIMP and BFast but it uses a different set of algorithms for the alignment. There's a cloud based web implementation (http://www.omixon.com/omixon/abouttoolkit.htm) where you can try it for free, and it's also available for free evaluation as a command line tool, you just need to send an email to [email protected].

[ECO]

If you're looking for aligners that find indels you could try the Omixon Variant Toolkit. It's a gapped aligner with spaced seeds similar to ShRIMP and BFast but it uses a different set of algorithms for the alignment. There's a cloud based web implementation (http://www.omixon.com/omixon/abouttoolkit.htm) where you can try it for free, and it's also available for free evaluation as a command line tool, you just need to send an email to [email protected].

Hi Tim,

This post is bordering on being too commercial for this forum...I'm going to let it stay here as it's relevant to the discussion but please just be aware in the future that overly commercial posts belong in the Vendor Forum. This was reported by a couple of people as too commercial.

Thanks!

-+Eric

[Tim Hague]

Hi Tim,

This post is bordering on being too commercial for this forum...I'm going to let it stay here as it's relevant to the discussion but please just be aware in the future that overly commercial posts belong in the Vendor Forum. This was reported by a couple of people as too commercial.

Thanks!

-+Eric

Hi Eric,

Thanks for the friendly warning, I'm fairly new here and just learning the rules of the road! I wasn't trying to sell anything, just trying to help the OP with his issue.

Cheers,

Tim.