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Pyclone User Group

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Andrew, … Irem Sarihan3

11/21/18

PyClone User Extensions

Hi, I have made a function that takes Mutect2 and TitanCNA outputs and converts them into Pyclone

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PyClone User Extensions

Hi, I have made a function that takes Mutect2 and TitanCNA outputs and converts them into Pyclone

11/21/18

6/5/23

Celleular prevalence or cancer cell fraction?

Hi all. I just reread the documentation on the GitHub page for Pyclone VI. Under the output format,

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Celleular prevalence or cancer cell fraction?

Hi all. I just reread the documentation on the GitHub page for Pyclone VI. Under the output format,

6/5/23

Lisa Wei, … Dalal Alsultan7

5/31/23

question about comparing two samples

Hi Andy, I am also comparing primary to met samples per patient. Has the link to instructions on how

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question about comparing two samples

Hi Andy, I am also comparing primary to met samples per patient. Has the link to instructions on how

5/31/23

6/6/22

Addition of Cellular prevalance in single sample not add up to 1?

Hello, We have longitudinal samples from the same patient. Samples were collected over time under the

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Addition of Cellular prevalance in single sample not add up to 1?

Hello, We have longitudinal samples from the same patient. Samples were collected over time under the

6/6/22

lyanliu, … Andrew5

10/28/21

Pyclone input file

My usual strategy for multiple samples is to call SNVs in each sample and filter for the high quality

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Pyclone input file

My usual strategy for multiple samples is to call SNVs in each sample and filter for the high quality

10/28/21

Yana Vassileva, Andrew2

8/10/21

PyClone Copy Number for normal sample

Hi Yana, 1. It is not a problem if the normal copy number is not always 2. We commonly use values of

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PyClone Copy Number for normal sample

Hi Yana, 1. It is not a problem if the normal copy number is not always 2. We commonly use values of

8/10/21

Zhuo Xm, Andrew4

4/14/21

Examples of major cn in pyclone-IV

That might be a bit noisy, but it should work. On Wednesday, March 17, 2021 at 7:12:32 PM UTC-7 xmz..

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Examples of major cn in pyclone-IV

That might be a bit noisy, but it should work. On Wednesday, March 17, 2021 at 7:12:32 PM UTC-7 xmz..

4/14/21

Andrew, … 危志庭5

4/13/21

PyClone-VI Released

Just major. But if you set major cn to the total copy and minor cn to zero it is nearly the same as

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PyClone-VI Released

Just major. But if you set major cn to the total copy and minor cn to zero it is nearly the same as

4/13/21

11033...@qq.com, Andrew6

2/22/21

Running Pyclone on panel-seq data with few mutations

Andy, thanks a lot for your quick reply. I'll try it! On Monday, February 22, 2021 at 10:11:10 PM

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Running Pyclone on panel-seq data with few mutations

Andy, thanks a lot for your quick reply. I'll try it! On Monday, February 22, 2021 at 10:11:10 PM

2/22/21

Chris B, Andrew2

11/20/20

config_extras_file argument

Hi Chris, It is best to use the setup_analysis command and then manually change the resulting config

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config_extras_file argument

Hi Chris, It is best to use the setup_analysis command and then manually change the resulting config

11/20/20

王浩, Andrew5

10/16/20

The difference between major_copy_number and parental_copy_number

Dear professor Andrew Roth Thanks for your reply! I encountered a new problem today ! I tried to

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The difference between major_copy_number and parental_copy_number

Dear professor Andrew Roth Thanks for your reply! I encountered a new problem today ! I tried to

10/16/20

5/8/20

YAML Load warning

Hello, I received the attached error when trying to run the pyclone code. I did not know the minor

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YAML Load warning

Hello, I received the attached error when trying to run the pyclone code. I did not know the minor

5/8/20

4/26/20

Preparing input file for pyclone

Hi Can anyone tell me, how can I prepare pyclone input files. I've vcf files from WES data and

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Preparing input file for pyclone

Hi Can anyone tell me, how can I prepare pyclone input files. I've vcf files from WES data and

4/26/20

henan zhu, Andrew2

1/21/20

WES and average depth ~100

Hi Henan, There is no real depth restriction. However, your ability to resolve clones will be limited

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WES and average depth ~100

Hi Henan, There is no real depth restriction. However, your ability to resolve clones will be limited

1/21/20

Pablo Eduardo García Nieto, Andrew3

12/12/19

Number of clusters (clones) linearly increases with number of mutations?

Thanks for the prompt response Andy! I'll implement those suggestions. Best, Pablo On Thursday,

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Number of clusters (clones) linearly increases with number of mutations?

Thanks for the prompt response Andy! I'll implement those suggestions. Best, Pablo On Thursday,

12/12/19

Rui Resende, Andrew2

10/23/19

Error creating PyClone plots

Hi Rui, If you using a lot mutations, the default plotting in PyClone will break. The best solution

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Error creating PyClone plots

Hi Rui, If you using a lot mutations, the default plotting in PyClone will break. The best solution

10/23/19

9/17/19

Commercial Licensing

From the pyclone github repo (https://github.com/aroth85/pyclone): "PyClone is free for academic

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Commercial Licensing

From the pyclone github repo (https://github.com/aroth85/pyclone): "PyClone is free for academic

9/17/19

Damjan Temelkovski, Andrew Roth3

9/3/19

Exception: No mutations found in common across samples. This commonly occurs when the muation_id field does not match for mutations in the input files. Search the user group before posting a message or a bug.

Hi Damjan, Yes that would be the issue. The samples have to be related, either from the same patient

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Exception: No mutations found in common across samples. This commonly occurs when the muation_id field does not match for mutations in the input files. Search the user group before posting a message or a bug.

Hi Damjan, Yes that would be the issue. The samples have to be related, either from the same patient

9/3/19

Rui Resende, Andrew3

7/29/19

ValueError: invalid literal for int() with base 10: 'ref_counts'

Indeed, one of my input files had a problem. Thank you very much! Best, Rui segunda-feira, 29 de

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ValueError: invalid literal for int() with base 10: 'ref_counts'

Indeed, one of my input files had a problem. Thank you very much! Best, Rui segunda-feira, 29 de

7/29/19

Davide Cittaro, Andrew2

7/29/19

Prevalence << 1 for clonal mutations in diploid regions...

Hi David, It is hard to know for certain. Try taking the lowest estimated cellularity values. If the

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Prevalence << 1 for clonal mutations in diploid regions...

Hi David, It is hard to know for certain. Try taking the lowest estimated cellularity values. If the

7/29/19

repick chen, Andrew2

7/29/19

question about major_cn in TSV input file

Hi Repick, The copy number of a mutation is the copy number of the overlapping CNV segment. You need

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question about major_cn in TSV input file

Hi Repick, The copy number of a mutation is the copy number of the overlapping CNV segment. You need

7/29/19

efa...@gmail.com, … Andrew Roth6

5/17/19

cellular prevalence estimation

Hi Stefano, There are two answers: 1) Just because the VAF is zero does not imply the prevalence is

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cellular prevalence estimation

Hi Stefano, There are two answers: 1) Just because the VAF is zero does not imply the prevalence is

5/17/19

Lisa Wei, Andrew2

4/29/19

Hi Lisa, 1) This table reports summary information for each cluster in each sample. The "size

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Hi Lisa, 1) This table reports summary information for each cluster in each sample. The "size

4/29/19

bioinf...@gmail.com, Andrew Roth4

4/18/19

What's the difference between parameters major_copy_number and parental_copy_number

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

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What's the difference between parameters major_copy_number and parental_copy_number

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

4/18/19

Luqman Hodgkinson, Andrew2

4/18/19

Incorporating Amplifications and Deletions into a PyClone Analysis

Hi Luqman, In principle you can use any variants for which ref/alt counts are available. The issue is

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Incorporating Amplifications and Deletions into a PyClone Analysis

Hi Luqman, In principle you can use any variants for which ref/alt counts are available. The issue is

4/18/19

David Zhang, Andrew2

4/18/19

PyClone 0.13.0 ZeroDivisionError: division by zero

Hi David, So it looks like the clustering part went well, but the post-processing is failing. I

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PyClone 0.13.0 ZeroDivisionError: division by zero

Hi David, So it looks like the clustering part went well, but the post-processing is failing. I

4/18/19

Young Soo Song, Andrew2

4/18/19

Is it possible to use ABSOLUTE results as input for tumor CNA?

I have never run ABSOLUTE, so I cannot comment on its outputs. Probably best to contact the authors

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Is it possible to use ABSOLUTE results as input for tumor CNA?

I have never run ABSOLUTE, so I cannot comment on its outputs. Probably best to contact the authors

4/18/19

11033...@qq.com, Andrew3

4/18/19

Clustering with Pyclone using pre-calculated CCFs

I have not tried running PyClone that way. In essence they are doing the genotype correction first

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Clustering with Pyclone using pre-calculated CCFs

I have not tried running PyClone that way. In essence they are doing the genotype correction first

4/18/19

edyta.k...@ardigen.com, Andrew2

4/18/19

PyClone parameters on simulated data

If the results are drastically different, then I would suggest running PyClone longer. My notes

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PyClone parameters on simulated data

If the results are drastically different, then I would suggest running PyClone longer. My notes

4/18/19

Tongwu Zhang, Andrew2

4/18/19

There seems to be some library incompatibility issues. Try creating a new conda environment and doing

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There seems to be some library incompatibility issues. Try creating a new conda environment and doing

4/18/19

Peter Ulintz, Andrew2

4/18/19

max_clusters error

The PyDP install is out of date. Try getting the latest version from the git repo https://github.com/

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max_clusters error

The PyDP install is out of date. Try getting the latest version from the git repo https://github.com/

4/18/19

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