Dear all, 

please would you advise, based on your experience, which algorithm is more reliable in confidently calling INDELS in cancer genomes (I am referring especially to INDELS of length > 50bp, let's say 50bp-500bp long). 

many thanks, 

-- bogdan 
pindel can do it but, when you get near to the 500bp mark, are you not then in the realm of small somatic copy number alterations? BBMap can also do this: https://www.biostars.org/p/254305/

In all cases, read length and insert size are obviously key.

Kevin