Question: a realiable algorithm that calls INDELS of length 50bp-300bp in cancer genomes
1
gravatar for Bogdan
10 months ago by
Bogdan690
Palo Alto, CA, USA
Bogdan690 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 • 442 views
ADD COMMENTlink modified 10 months ago by Eric T.2.3k • written 10 months ago by Bogdan690

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 10 months ago by Bogdan690

Replied above!

ADD REPLYlink written 10 months ago by Kevin Blighe35k
4
gravatar for Kevin Blighe
10 months ago by
Kevin Blighe35k
Republic of Ireland
Kevin Blighe35k 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 10 months ago by Kevin Blighe35k

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

ADD REPLYlink written 10 months ago by Kevin Blighe35k

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 10 months ago • written 10 months ago by Bogdan690
1
gravatar for Eric T.
10 months ago by
Eric T.2.3k
San Francisco, CA
Eric T.2.3k wrote:

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

ADD COMMENTlink written 10 months ago by Eric T.2.3k

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 10 months ago • written 10 months ago by Bogdan690
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