Seq2Karyotype is a tool designed for copy number alterations analysis and karyotyping using bulk whole-genome sequencing data. This README provides instructions for installation, configuration, and usage of Seq2Karyotype, along with examples and helpful tips.
Download the package, then follow the instructions below.
# setup the virtual environment
conda -create -n s2k python=3.11 pandas=1.5.2 shiny==0.6.0
# activate the virtual envrionment
conda activate s2k
# install the package
cd /path/to/download/folder
pip install Seq2Karyotype
CytoBand annotation are provided in the folder aux. You will have to download the SNP whitelist yourself. Both lists for hg19, hg38 are provided under https://drive.google.com/drive/folders/1ontR5R_dfl8uJc50PwHA2hxEBIcdkmn7?usp=drive_link. You can use your own SNP list if you wish, just make sure to follow the same format as in the provided files.
- Convert your variant calling file to allele count format.
An example script for converting gVCF file is provided below
#!/bin/bash
filename=$( echo $1 | cut -d'/' -f12 | cut -d'.' -f 1 )
echo $filename
zcat -1 $1 | grep -v -e '#' | grep AD | awk 'BEGIN {print "Chr\tPos\tRef\tAlt\tType"};{split($10,a,":"); split (a[2],b,","); if (length(b) == 3) print $1"\t"$2"\t"b[1]"\t"b[2]"\tSNP"}' > $filename.ac
The output allele count file should contain at least five columns
| chromosome | position | reference_count | alternative_count | type |
|---|---|---|---|---|
| chr1 | 10513 | 12 | 3 | SNP |
| chr1 | 13868 | 1 | 6 | SNP |
| chr1 | 14464 | 7 | 35 | SNP |
- Get a local copy of the configuration file.
s2k getconfig
-
Edit the
[Input]and[InputColumns]sections in the configuration file to suit your data. We don't recommend changing additional parameters when starting out. -
Run S2K to generate output files.
s2k analyze -i sample_name.txt -c your_configuration_file.ini -s sample_name -m0 diploid_coverage -mc merging_coeff
... Lots of log info! ...
12:18:19 S2K.WGS: INFO: Ready to report!
All done
Note that m0 and mc are optional. m0 will be calcuate by the diploid detection algorithm, and can be adjusted if incorrect. mc is the merging parameter that controls the merge between segements.
There will be 4 output files in total:
sample_name.bed: The main output file contains the segmentation information.
sample_name.dat.gz: The output for individual chromosome information.
sample_name.log: Your good old log file.
sample_name.par: The parameters used including reference diploid coverage, karyotype models, etc,.
- Launch the viewer for visualization.
# if you are running this on your local machine, such as a desktop or laptop:
s2k viewer
# if you are running this on a remote machine, like a cluster:
s2k viewer --remote
**********
Access dashboard in browser via: http://10.220.16.129:39738
**********
INFO: Started server process [11716]
INFO: Waiting for application startup.
INFO: Application startup complete.
INFO: Uvicorn running on http://10.220.16.129:39738 (Press CTRL+C to quit)
Load the output files
If you find this tool useful, please star this repo and cite our paper (when it comes out) :)
Limeng Pu et al. "Seq2Karyotype (S2K): A method for deconvoluting heterogeneity of copy number alterations using single-sample whole-genome sequencing data" [abstract]. Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7419
This README file is written by Limeng Pu.