Searching For Cnv (Copy Number Variation) Tools

Question

[youngcsong]

Hi,

I am currently searching for CNV tool that works with BAM or FASTQ files as an input. Our group is currently using a pipeline that requires the tumour content of the sample be provided as a parameters. We would like the tool to instead estimate the tumour content for us, as most estimates from pathologists are inaccurate, and requires multiple runs. Also, we would like our tool to estimate the ploidy of the tumour samples (e.g. whether the tumour is triploid, quadriploid, etc.).

I found some tools such as CNANorm through Google search, but was wondering if there is anything better out there. Your input would be much appreciated. Thank you.

Young

[Vikas Bansal]

May be Control-FREEC could help.

Answer 1

[Alex Paciorkowski]

I'm not sure about estimating the tumor content, but Pindel is a tool that does a reasonable job on data files with complex indels.