Call all insertions and deletions in bam file

Question

[Mick]

Hi, I have a file with ultra-deep sequencing data of a 100bp genomic region that has been sequenced 1M times. (I have posted about this before). I aligned the reads to the genome with bwa.

I'm looking for a tool that will call ALL insertions and deletions without any filtering. I will set my own cut-offs later. Ideally I'd like something close to the output of igvtools (--bases):

Pos         A       C       G   T       N       Del Ins
30223844    193     745858  19  255     1087    3   0
30223845    745973  4       97  68      1270    3   0
30223846    53      73      6   746264  1004    15  0
30223847    112     81      7   745742  1473    0   4
30223848    746167  7       288 62      832     59  0
30223849    746535  5       91  48      735     1   0
30223850    746182  5       66  21      1141    0   0
30223851    59      66      0   731636  15654   0   0

Now unfortunately igvtools only outputs the number of deletions and insertions at a given position. However I also need the exact bases that have been inserted or deleted, and how many times this indel occured. Like this:

Del                       Ins
19:ACT,5:AC,3:AGTC        11:AAG

Is anyone aware of a programm that does this? Thank you very much in advance, happy new year to all!

[Mick]

I tried bbmap's callvariants today, but it only found around 30 indels, but there should be much more than that. Can anyone please suggest a tool, that outputs all indels in a file? This seems like the most basic task.

[ATpoint]

Did you try to most common tools like bcftools, pindel, delly? All these tools have some filters as this is what makes them sophistocated variant callers that distinguish true events from noisy/artifact calls. I would be careful to alter the filters.