Use DeepSomatic for FFPE Low-Pass Sequencing (LPS) WGS Tumor-only Samples
Hi,
I have 10 Low-Pass Sequencing (0.05 x - 0.1 x coverage) WGS of FFPE Prostate Cancer (PCa) tumor-only tissues, which I intend to run for somatic variant calling. I recently became aware of DeepSomatic and would like to test it on my LP-WGS samples. My queries are:
1) You already provided a case study for FFPE WGS tumor-only somatic variant calling. Will this be suitable for the LPS samples with ultra-low coverage that I have mentioned?
2) You have used a high-confidence region bed file and the `high-confidence_sINDEL_sSNV_in_HC_regions_v1.2.1.merged.vcf.gz` file. Is this the default PON VCF file? So, in my understanding, as I only want to filter germline variants by default, I need to keep `--use_default_pon_filtering=true`. Is it right?
NOTE: I already have aligned and sorted BAM files to the GRCh38 reference.
Thanking you,
Soham
关闭于 2025-10-21 2 条评论