SOAP2 and deletions/insertions

[KaiYe]

How about bwa-maq (http://bio-bwa.sourceforge.net/bwa.shtml), Pindel(seems not available now)

Pindel is still being actively updated.
http://www.ebi.ac.uk/~kye/pindel/release/
New version of Pindel is being tested with the following additional functions:
1. Allow sequence errors/SNPs in the same reads containing INDELs/SVs
2. non-template sequence in deletions
3. inversions
4. tandem duplications
5. breakpoints of large insertions

[drio]

Well, I can tell you the following.

I have simulated loads of data. I have generated datasets with more than a billion reads where error profiles/PCR errors/sequencing errors were simulated and acted as a background for real SNPs that needed to be discovered. The real SNPs always come out on top. So far so good, but with deletions/insertions, I am completely confused.

Indeed, the manual/documentation is not clear. Did you have any success contacting the authors?

In your simulations do you introduce indels or it is only single base changes?
How does that affects your results?

[dingxiaofan1]

Bwa-maq

How about bwa-maq (http://bio-bwa.sourceforge.net/bwa.shtml), Pindel(seems not available now)

[joa_ds]

I just checked out their site and found the following thing.

SOAPindel: SOAPindel is developed to find the insertion and deletion specially for re-sequence technology : Coming soon.

I am just wondering if indel detection is already included in SOAP2? Has anyone ever seen an indel being detected by using SOAP2?

[francesco.vezzi]

Well, I can tell you the following.
Indeed, the manual/documentation is not clear. Did you have any success contacting the authors?

Yes I contact them more than once.... but they never reply...
It is really strange that the most used aligner (or at least one of the most used) is so obscure.....

[joa_ds]

Well, I can tell you the following.

I have simulated loads of data. I have generated datasets with more than a billion reads where error profiles/PCR errors/sequencing errors were simulated and acted as a background for real SNPs that needed to be discovered. The real SNPs always come out on top. So far so good, but with deletions/insertions, I am completely confused.

Indeed, the manual/documentation is not clear. Did you have any success contacting the authors?

[francesco.vezzi]

Hi
I can't help you so much but I can report another strange behaviour of SOAP2. Despite the fact that you vary the -v option that is the total amount of errors (mismatches) allowed in one read the output that you obtain is always the same. I Try to change several parameters like the seed length without understand how to specify an exact number of errors.

Despite the fact that SOAP2 is one of the most used aligners it has some troubles: there is no a clear documentation, the source code is not available and hence we actually don't know what kind of heuristics are applied in order to speed up the query time...

Francesco

[joa_ds]

I was told that SOAP should be able to detect deletions and insertions up to 3bp.

So i made a reference file and a file with a normal read and some reads with 1,2,3 bp deleted and inserted. Just to test how the output format etc would look like and to get optimal parameter settings.

i have used different -e settings etc, but it appears that not a single read with deletion/insertions gets aligned...

All i get is

Begin Alignment ...
8 ok 0.00 sec
Total Reads: 8
Alignment: 1 (12.50%)

-> Only the normal read gets aligned...

Is there a secret parameter i should set somewhere?