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: gatk
4 posts
How to Run a Somatic Variant Calling Pipeline on Your Own Sequencing Data
A working pipeline for calling somatic SNVs and indels with GATK Mutect2, from BAM to filtered, annotated VCF, plus what the results mean at low variant allele fraction and where the method stops working.
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 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.