Dear all I've a big problem with samtools mpileup since I am trying to retriving base counts and indel but fails to locate indels. More in particular, it seems that INDELs are shifted by one position (i.e. if the deletion is located at position 2, samtools gives me that is at position 1).
I've tryied bam-readcount to do the same task and it calls INDEL at the right position (after check it with IGV).
What I've tryied so far is:
- Using different samtools versions: nothing changes
- Using different machines: nothing changes
I would like to ask you if it is a well known bug that others found or it's just me.
I know that I could pharse the output with awk shifting indels, but I prefer not to "touch" data in that sense. Thank you in advance for your help