Question

Ploidy in WGS samples

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2.9 years ago

loy_loy ▴ 10

Hi everyone,

I am working with WGS cancer datasets. I downloaded the data as bam files from GDC TCGA. I want to know if there is a program to find out the ploidy of the samples.

Thank you!

Best

Lynn

cancer WGS NGS bam ploidy • 895 views

ADD COMMENT • link updated 2.8 years ago by Thind amarinder ▴ 340 • written 2.9 years ago by loy_loy ▴ 10

score 0 · Answer 1 · 2022-03-01

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2.8 years ago

Zhenyu Zhang ★ 1.2k

There are PanCan papers published a few years ago that contain ABSOLUTE analysis. You might want to just search for PanCan in the GDC publication pages. Ploidy data is probably in one of the attachment there.

ADD COMMENT • link 2.8 years ago by Zhenyu Zhang ★ 1.2k

score 0 · Answer 2 · 2022-03-01

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2.8 years ago

Thind amarinder ▴ 340

may be you would like to try https://github.com/hartwigmedical/hmftools/blob/master/purple/README.md

ADD COMMENT • link 2.8 years ago by Thind amarinder ▴ 340