empty result when using cellsnp-lite

[onmyojiyys]

Thank you very much for your research in the field of CNA analysis. I have encountered some issues while using CalicoST. When I executed cellsnp-lite with three samples (10x Genomics Visium v2), the output files were all empty, and no SNPs were identified. Could you provide a download link for the bam files in the examples data? I need to confirm whether the issue is with my usage of CalicoST or the data itself. Best regards!

cellsnp-lite -s /disk/pipeline/STtools/CNV/calicost/MU_4174_F1-0829/possorted_genome_bam.bam -b /disk/pipeline/STtools/CNV/calicost/MU_4174_F1-0829/barcodes_change.txt -O /disk/pipeline/STtools/CNV/calicost/MU_4174_F1-0829/genotyping/ -p 20 --minMAF 0 --minCOUNT 1 --UMItag Auto --cellTAG CB --gzip

[Congm12]

The command for cellsnp-lite lacks -R argument for specifying the VCF file of the known SNPs for genotyping. The VCF of known human SNPs can be obtained from the https://cellsnp-lite.readthedocs.io/en/latest/main/data.html#data-list-of-common-snps.

In addition, can you check whether your SRT samples are probe-based? As probe-based transcriptomics doesn't contain SNP information, we recommend running STARCH (https://github.com/raphael-group/STARCH/tree/develop) or other total copy number inference methods.

[onmyojiyys]

Thank you. After adding candidate SNPs with the -R parameter, the results I obtained are still empty. My data is Visium FFPE, captured with probes.
After downloading the data from the 10x database and completing the analysis with spaceranger count, the calicoST pipeline is running normally.

[onmyojiyys]

The data used were human lung cancer samples, and the data summary report is as follows.

When running the estimate_tumor_proportion.py script, some errors were encountered and a response is hoped for.

Issue with the MIN_TOTAL parameter in the identify_normal_spots function
The configuration_purity configuration file is as follows:

When using the default parameters, the following error occurred. Is it because the MIN_TOTAL parameter is set too high, resulting in this_bafs being empty? If so, does this mean the data is not suitable for analysis with the CalicoST method, or can the MIN_TOTAL threshold be appropriately lowered?

The default MIN_TOTAL is set to 10. When setting MIN_TOTAL to 2 and rerunning, the same error still occurred.

[Congm12]

Hi,

Probed-based spatial transcriptomics data does not provide the SNP information. We recommend using the total copy number inference methods such as STARCH (https://github.com/raphael-group/STARCH/tree/develop) and inferCNV (https://github.com/broadinstitute/infercnv).