Running HiScanner with Demo Data

Download this repository by

git clone https://github.com/parklab/hiscanner_demo.git
cd hiscanner_demo

1. Download and Extract Demo Data

# Download from Figshare
wget https://figshare.com/ndownloader/articles/28369088?private_link=c5aeb5bc039a2990fc89
mv '28369088?private_link=c5aeb5bc039a2990fc89' demo_data.zip

wget https://figshare.com/ndownloader/articles/28375844?private_link=854df579f68882779a06
mv '28375844?private_link=854df579f68882779a06' fasta_split.zip

Extract the downloaded files using unzip

# Extract all files
unzip demo_data.zip && tar -xvf scan2_out.tar.gz
unzip fasta_split.zip
rm demo_data.zip scan2_out.tar.gz fasta_split.zip
cd fasta_split && for tarfile in *.tar.gz; do
    tar -xzvf "$tarfile"
done
cd ..

2. Initialize Project

# Activate environment
conda activate hiscanner_test

# Initialize (choose one)
hiscanner init # then edit config.yaml
# OR use the provided config.yaml
cp resources/config.yaml .
# remember to edit the config.yaml file to set the correct paths

3. Validate Setup

hiscanner validate

Expected output:

INFO     ✓ Configuration validated successfully
INFO     ✓ Output directories can be created
WARNING  Missing Raw variants VCF MD5: scan2_out/gatk/hc_raw.mmq60.vcf.gz.md5
WARNING  Missing Phased hets VCF MD5: scan2_out/shapeit/phased_hets.vcf.gz.md5
INFO     ✓ SCAN2 outputs validated successfully
INFO     ✓ bcftools validated successfully
INFO     ✓ samtools validated successfully
INFO     ✓ R and mgcv package validated successfully
INFO     All validation checks passed successfully!

4. Run Pipeline Steps

Step 1: SNP Calling

hiscanner run --step snp

Expected output:

INFO     Running snp step...
INFO     Preparing SNP calling results
WARNING  Missing Raw variants VCF MD5: scan2_out/gatk/hc_raw.mmq60.vcf.gz.md5
WARNING  Missing Phased hets VCF MD5: scan2_out/shapeit/phased_hets.vcf.gz.md5
INFO     SNP calling results prepared successfully
INFO     ✓ Pipeline completed successfully

Step 2: Phasing

hiscanner run --step phase

Expected output:

INFO     Running phase step...
INFO     Starting phasing step
WARNING  Missing Raw variants VCF MD5: scan2_out/gatk/hc_raw.mmq60.vcf.gz.md5
WARNING  Missing Phased hets VCF MD5: scan2_out/shapeit/phased_hets.vcf.gz.md5
INFO     Processing 3 cells
INFO     Running bcftools query for SRR6204923_Lymphocyte-068
INFO     Running bcftools query for SRR6204878_Lymphocyte-015
INFO     Running bcftools query for SRR6204925_Lymphocyte-066
[... Processing details ...]
INFO     Results saved for SRR6204878_Lymphocyte-015
INFO     Results saved for SRR6204923_Lymphocyte-068
INFO     Results saved for SRR6204925_Lymphocyte-066
INFO     Phasing step completed successfully
INFO     ✓ Pipeline completed successfully

Step 3: ADO Analysis

hiscanner run --step ado

Expected output:

[... Processing details ...]
INFO     ADO analysis completed successfully
INFO     ✓ Pipeline completed successfully

Step 4: Normalization

hiscanner run --step normalize

Expected output:

INFO     Running normalize step...
INFO     Starting normalization pipeline
INFO     Workflow setup completed in /home/yzhao/demo/hiscanner_out/.workflow
INFO     Running normalization workflow from /home/yzhao/demo/hiscanner_out/.workflow

Step 5: Segmentation

hiscanner run --step segment

Expected output:

INFO     Running segment step...
INFO     Starting segmentation
INFO     Running multisample segmentation
INFO     Processing lambda=2
[... Processing details for each lambda value and chromosome ...]
INFO     Successfully saved combined segments for 3 cells at lambda=2048
INFO     Segmentation completed successfully

Step 6: CNV Calling

hiscanner run --step cnv

Expected output:

INFO     Running cnv step...
INFO     Starting CNV calling pipeline
INFO     Using standard (RDR + BAF) mode
INFO     Saving final calls to hiscanner_out/final_calls
INFO     Processing cell SRR6204923_Lymphocyte-068
[... Processing details for each cell ...]
INFO     Generating visualizations
INFO     HiScanner CNV calling pipeline completed successfully
INFO     ✓ Pipeline completed successfully

5. Clean Up (Optional)

hiscanner clean

Expected output:

INFO     ✓ Removed directories: cfg, segcfg, readpos, temp

Now you can explore the results in the hiscanner_out directory!

You can compare the genome tracks in final_calls with resources/hiscanner_out_expected/final_calls/*png. They should be identical. There are two diploid cells and one cell with chr2 loss and chr16 gain.

Important Note: The BAF signals are not derived from real mouse scWGS data but rather simulated. As this mouse strain is not cross-bred, there are almost no heteterozygous SNPs. The purpose of this demo is for users to check installation and explore the pipeline's functionality, not to demonstrate real biological results.