I need allele copy number information for running PyClone

Question

[a01039012387]

Hello. I'm new with pyclone and I'm trying to run a pyclone with WES data from TCGA. I need some information of allele specific copy number to make a input file for pyclone, but i don't know which tools I can use for it. I downloaded somatic mutation output of mutect file from TCGA and it has t_depth/t_ref_count/t_alt_count/n_depth, but there is no information about parental copy informaitons.

could you recommend any tools for find specific copy number data? And should I use the location only has 2 copies for pyclone?

Thank you.

Answer 1

[Eric T.]

TCGA also provides copy number as SEG files, which indicate log2 ratios but not absolute integer copy number or allele-specific copy number. But you can use CNVkit along with a properly formatted VCF file to get allele-specific copy number with the import-seg and call commands. Some reformatting with pandas/R/Excel will still be necessary; I'm not aware of a direct way to coerce the TCGA data to PyClone's input format all in one shot.

You can also get the TCGA copy number data in a slightly friendlier form from cBioPortal.

Answer 2

[nilesh.gardi2688]

How to infer allele specific copy number from DNAcopy package output or any SNP array segmentation data? I also need to run Pyclone for which I need allele specific copy number. I have exome data as well affymetrix SNP array data for same samples.

Answer 3

[firatuyulur]

I used sequenza. In my case I had both tumour and normal bams.