Question: I need allele copy number information for running PyClone
gravatar for a01039012387
2.2 years ago by
a0103901238710 wrote:

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.

ADD COMMENTlink modified 11 days ago by firatuyulur290 • written 2.2 years ago by a0103901238710
gravatar for Eric T.
2.1 years ago by
Eric T.2.5k
San Francisco, CA
Eric T.2.5k wrote:

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.

ADD COMMENTlink written 2.1 years ago by Eric T.2.5k
gravatar for nilesh.gardi2688
20 months ago by
nilesh.gardi26880 wrote:

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.

ADD COMMENTlink written 20 months ago by nilesh.gardi26880
gravatar for firatuyulur
11 days ago by
firatuyulur290 wrote:

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

ADD COMMENTlink written 11 days ago by firatuyulur290
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