Integrated SNP
Identification Pipeline

A comprehensive web-based platform for identifying Single Nucleotide Polymorphisms (SNPs) from genomic data. Seamlessly integrate alignment, variant calling, and annotation into a single automated pipeline.

Start Analysis User Manual

# Running ISNIP-2026 Core Pipeline...

[INFO] loading hg38 reference genome...

[INFO] indexing chromosome regions...

bwa-mem2 mem -t 8 index/hg38 sample_R1.fq sample_R2.fq

[BWA] 98.4% reads mapped. samtools sort output...

gatk HaplotypeCaller -R index.fa -I sorted.bam -O raw.vcf

[GATK] 4,152 raw SNPs detected. hard filters applying...

snpeff ann -v ClinVar_2023-Oct filtered.vcf > final.vcf

[SUCCESS] Annotation mapping completed.

AGY ENGINE V2.0

Workflow Architecture

Precision Pipeline Modules

Alignment

High-throughput read mapping against reference genomes using industry-standard BWA-MEM or Bowtie2 algorithms with optimized parameters for clinical accuracy.

View Alignment Specs

Variant Calling

Precision detection of germline and somatic SNPs using GATK HaplotypeCaller or DeepVariant. Supports multi-sample joint genotyping for population studies.

Algorithm Documentation

Annotation

Functional interpretation of variants using VEP and SnpEff, cross-referenced against ClinVar, dbSNP, and gnomAD databases for clinical relevance.

Database Catalog

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