Question: estimate tumor purity from target capture sequencing
1
gravatar for lffu_0032
17 months ago by
lffu_003260
lffu_003260 wrote:

hi, everyone, is there a good way to estimate the tumor purity from target capture sequencing?i need to calculate the copy number and without the purity, the CN may be not accurate. thanks for your kind help.

ADD COMMENTlink modified 17 months ago by dariober11k • written 17 months ago by lffu_003260
0
gravatar for dariober
17 months ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

The facets package detects copy number variants and gives you the purity and ploidy estimates.

If interested, I also wrote a wrapper to run the analysis as a single line command, see cnv_facets.

ADD COMMENTlink written 17 months ago by dariober11k

thank you. i see that the facet is suit for tumor-normal pair calling, but i have only tumor-only capture data...

ADD REPLYlink written 13 months ago by lffu_003260
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