dindel and bioscop: someone did it?

[tdm]

Hello,
I am using bioscope to align reads (solid), and get a bam file with matobam tool from this software.
I wanted to try dindel and compare results with the build in plugin, but I did not get any results: 0 kb files from the phase1 (extract indels from bam file).

My question is:
Did someone already tried dindel with bam files from bioscope ?
Was it successful ?

thx for the information

Thibault

[drio]

I haven't used dindel but it should not matter what tool you use to perform the alignments. That
is what the SAM format isfor. Does the tool come with any data for testing? If so, look at the
bam (or sam) they use and compare it with your BAM from bioscope.

[tdm]

No, there was no testing data coming with the tool. SO i assume maybe indel was lookin for an information not present.
I had an issue like that with samtools looking for XS information, but last version solve this.