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Welcome to Sequenza User Group!!
Feel free to ask questions and expose your problems/difficulties using sequenza.
Proposal and ideas are welcome as well.

Enjoy!!

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Amit Goyal, … Tom Clark25

2:20 AM

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Xin Zheng, … YanLemon5

Apr 1

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Francesco Favero

Jan 27

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Jan 27

12/16/25

seqz_binning not reducing file size with high-coverage WGS data (>150x) + segmentation fault

Hello, I'm experiencing issues with sequenza-utils on high-coverage whole-genome sequencing data

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seqz_binning not reducing file size with high-coverage WGS data (>150x) + segmentation fault

Hello, I'm experiencing issues with sequenza-utils on high-coverage whole-genome sequencing data

12/16/25

Davide Cittaro, Michael Knudsen5

5/15/25

Memory error (paste exceeding 2^31-1 bytes)

I have had the same issue (it happens for noisy samples), and I've located the problem to this

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Memory error (paste exceeding 2^31-1 bytes)

I have had the same issue (it happens for noisy samples), and I've located the problem to this

5/15/25

virginia gazziero

5/13/25

Errors including r-sequenza in bioconda recipe

Hi, Thanks for the package! I am currently working at the development of a nf-core pipeline, and to

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Errors including r-sequenza in bioconda recipe

Hi, Thanks for the package! I am currently working at the development of a nf-core pipeline, and to

5/13/25

NILESH MUKHERJEE, Francesco Favero2

3/19/25

Sequenza v4.0.0 Error/Issue Debugging help required

Hi Nilesh, I've messed up adding some optimization working only in my laptop, which uses clang to

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Sequenza v4.0.0 Error/Issue Debugging help required

Hi Nilesh, I've messed up adding some optimization working only in my laptop, which uses clang to

3/19/25

2/8/25

How to use sequenza to detect focal homozygous deletions

Hi, I am preparing to work on a project to call CNV events in a number of WES tumor -normal pairs.

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How to use sequenza to detect focal homozygous deletions

Hi, I am preparing to work on a project to call CNV events in a number of WES tumor -normal pairs.

2/8/25

Michael Knudsen2

11/28/24

Corner case bug in sequenza.results?

Hi, Quick update on this issue. I have managed to get around it by adding seg.tab <- seg.tab[seg.

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Corner case bug in sequenza.results?

Hi, Quick update on this issue. I have managed to get around it by adding seg.tab <- seg.tab[seg.

11/28/24

Tusharika Rastogi

11/11/24

Sequenza.extract ERROR

Hello, I am trying to use the sequenza.extract function to process the seqz data. I produced the seqz

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Sequenza.extract ERROR

Hello, I am trying to use the sequenza.extract function to process the seqz data. I produced the seqz

11/11/24

Fenisha Shah, favero.f...@gmail.com3

6/27/24

Installation error with the latest version of sequenza

Hello Francesco That seems to work! Thank you for your prompt response. I would like to highlight

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Installation error with the latest version of sequenza

Hello Francesco That seems to work! Thank you for your prompt response. I would like to highlight

6/27/24

6/22/24

Sequenza ERROR: Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)

Hi I am using Sequenza to identify CNAs in tumor-normal files . A year ago I was able to generate the

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Sequenza ERROR: Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)

Hi I am using Sequenza to identify CNAs in tumor-normal files . A year ago I was able to generate the

6/22/24

6/14/24

Unable to install sequenza on any version of R.

install.packages('sequenza') will not work after multiple tries on various distros. Any ideas

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Unable to install sequenza on any version of R.

install.packages('sequenza') will not work after multiple tries on various distros. Any ideas

6/14/24

rkendar, … Michael Knudsen6

6/12/24

Sequenza failed >100 GB RAM

Yup, it works fine. I'm running it in production without any issues. I'm using a conda

unread,

Sequenza failed >100 GB RAM

Yup, it works fine. I'm running it in production without any issues. I'm using a conda

6/12/24

Giorgia Gandolfi, Davide Cittaro2

5/29/24

bam2seqz only processes one chromosome

Do the two input file have the same chromosome order? I had similar issue recently and realized that

unread,

bam2seqz only processes one chromosome

Do the two input file have the same chromosome order? I had similar issue recently and realized that

5/29/24

Michael Knudsen

5/29/24

Adjusted depth ratios before segmentation

Hi, Is it possible to make Sequenza output adjusted depth ratios at all SNP positions before

unread,

Adjusted depth ratios before segmentation

Hi, Is it possible to make Sequenza output adjusted depth ratios at all SNP positions before

5/29/24

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