Building a SNP Calling Pipeline for Your Own Whole Genome
A step-by-step pipeline from raw FASTQ to a filtered, benchmarked VCF for a single human genome, with the tool choices, parameters, and quality checks we would use.
Tag: deepvariant
4 posts
SNP Calling Tools: Which One to Run on Your Own Genome
A practical comparison of DeepVariant, GATK HaplotypeCaller, bcftools mpileup, Strelka2, and Clair3 for calling SNPs from your own whole-genome data, with commands, benchmarks, and the failure modes that matter.
Calling SNPs From Your Own Whole-Genome Sequencing Data
A step-by-step guide to going from raw FASTQ to a filtered, benchmarked, annotated single-sample VCF, with the tools, flags, and quality numbers we would use ourselves.
Calling Variants From Your Own Whole-Genome Sequencing Data
A working end-to-end guide to going from FASTQ to a filtered, benchmarked VCF on a personal 30x human genome, with the specific tools, flags, reference files, and failure modes we would use.