What's the difference between parameters major_copy_number and parental_copy_number

[bioinf...@gmail.com]

Hi Andrew, 

Is there a difference between parameters major_copy_number and parental_copy_number?

I have major and minor copy number data, what should I set for --prior?

Best regards,

Shangyi Luo

[Andrew]

Hi Shangyi,

There is a subtle difference, essentially major_copy_number is a slightly vaguer prior. I think it is the most appropriate prior in general, hence it is the default. So I would suggest using major_copy_number.

Cheers,

Andy

[bioinf...@gmail.com]

Dear professor Andrew Roth,

I have another question. We used exome data from TCGA that have limited sequencing depth. How to set for parameter --density. Is it best to choose pyclone_binomial? OR pyclone_beta_binomial?

I 'll be appreciated it if you could take the time to answer my questions. 

Best regards,

Shangyi Luo

在 2019年4月17日星期三 UTC+8下午2:33:54，bioinf...@gmail.com写道：

[Andrew Roth]

If the depth is less than 100x or do the Binomial will be fine. For higher depth use the Beta Binomial.

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