FAQ

General

1) Where can I access the latest SCI-VCF source code?

You can access the source code via the GitHub link.

2) How can I report bugs and suggest improvements in SCI-VCF?

You can post your bugs and suggestions here.

3) How do I cite SCI-VCF?

Venkatesh Kamaraj, Himanshu Sinha, SCI-VCF: a cross-platform GUI solution to summarize, compare, inspect and visualize the variant call format, NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae083, https://doi.org/10.1093/nargab/lqae083

4) Is the online version of SCI-VCF hosted on a HIPAA-compliant infrastructure?

The online version of SCI-VCF is on shinyapps.io, currently hosted on Amazon’s Web Services (AWS) infrastructure in the US-east-1 region. The infrastructure used is not the HIPAA-compliant stack, and users must take care to upload only anonymized and appropriate data.

To work with sensitive data, we recommend a local installation of SCI-VCF in a user-controlled infrastructure.

Installation

Conda

5) How to install SCI-VCF in Windows OS using conda?

Step 1. Install WSL. Documentation
Step 2. Install Miniconda inside WSL. Reference
Step 3. Install MobaXterm Home edition. It is a free software that offers an enhanced terminal for Windows with an X11 server. Documentation
Step 4. Open a WSL terminal inside MobaXterm (Open MobaXterm --> Click on Sessions --> New Sessions --> WSL --> Select Linux distribution --> OK) Step 5. Follow the instructions for Conda-based installation on the installation page

Docker

6) How to run the Docker container as a detached backend job and keep SCI-VCF always active?

Run the docker image in detached mode.

sudo docker run -d --rm -p 3000:3000 venkatk89/sci-vcf

Now, SCI-VCF will always be active at http://0.0.0.0:3000/

7) How to solve ‘docker: Got permission denied while trying to connect to the Docker daemon socket at unix’ error while installing SCI-VCF with Docker?

Add your user to the docker group

sudo usermod -a -G docker username

If the issue persists, the socket file can be made available to everyone instead of just the users in the docker group.

sudo chmod 666 /var/run/docker.sock

8) How to solve ‘xhost: unable to open display “:0”’ while Docker installation of SCI-VCF?

xhost local:docker

Customization

9) How to increase the default upload size?

Note: File upload size cannot be altered in the online version of SCI-VCF. It can only be done in the local/remote installation/deployments.

Open R/global.R file in RStudio. Go to Line #27

#set maximum file upload size in Shiny to 1 GB
options(shiny.maxRequestSize = 1 * 1024^3) 

Edit the upload file size according to your requirements.

10) How to change the default file processing steps? Open R/summarize_vcf.R. Go to Line #4

break_multiallelic_sites = TRUE, remove_duplicated_entries = TRUE

Disable the parameters according to your requirements.

Output VCF files

11) Issues with SCI-VCF outputted VCF files?

While the VCF format is conserved in the output file, the compression algorithm used is parallelized and is not gzip-based. Recent VCF processing software requires their input VCF files to be gzipped. To overcome this, decompress and recompress the SCI-VCF output VCFs using a gzip-based compressing algorithm:

gunzip sci-vcf_output.vcf.gz

gzip sci-vcf_output.vcf