Question: a realiable algorithm that calls INDELS of length 50bp-300bp in cancer genomes
1
gravatar for Bogdan
3 months ago by
Bogdan510
Palo Alto, CA, USA
Bogdan510 wrote:

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

cnv snv sv indel • 226 views
ADD COMMENTlink modified 3 months ago by Eric T.2.2k • written 3 months ago by Bogdan510

Thank you Kevin. I have been inspecting cgpPINDEL : https://github.com/cancerit/cgpPindel, as they provide also a docker container. Please would you let me know : is cgpPINDEL largely equivalent to PINDEL ? Thanks !

ADD REPLYlink written 3 months ago by Bogdan510

Replied above!

ADD REPLYlink written 3 months ago by Kevin Blighe21k
4
gravatar for Kevin Blighe
3 months ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k wrote:

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: detect large indels

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

Kevin

ADD COMMENTlink written 3 months ago by Kevin Blighe21k

Yes, cgpPindel just appears to be wrapper of Pinel. Looks good.

ADD REPLYlink written 3 months ago by Kevin Blighe21k

thanks a lot Kevin ! may I add, have you used it extensively ? does it require a lot of filtering of the VCF files in order to get the reliable variants ?

ADD REPLYlink modified 3 months ago • written 3 months ago by Bogdan510
1
gravatar for Eric T.
3 months ago by
Eric T.2.2k
San Francisco, CA
Eric T.2.2k wrote:

LUMPY and Manta do well in this range, provided you have sequencing coverage around the relevant breakpoints.

ADD COMMENTlink written 3 months ago by Eric T.2.2k

thank you Eric. good to hear from you ! please would you have any comments about DELLY, how well it does to call the INDELs in 30-300 bp range ? thanks.

ADD REPLYlink modified 3 months ago • written 3 months ago by Bogdan510
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