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!
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.
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.