GATK variant calling (Pieridae)

Knowledge graph centered on GATK variant calling (Pieridae) with 44 nodes and 135 connections. Top connected: Ligusticum porteri, Atriplex canescens, Lepidoptera, Populus, Boechera stricta.

Method synopsis

Bioinformatics pipeline for processing raw sequencing reads through quality filtering, mapping, variant calling, and SNP filtering using GATK v4.0 and associated tools.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Patterns of genetic variation and local adaptation of a native herbivore to a lethal invasive plant (2024), Molecular Ecology. Implementations in other papers (listed below) may differ.

1. SNP calling and filtering
   Raw reads trimmed using fastp, mapped to reference genome using bwa mem, variants called using GATK v4.0. Quality filtering applied: QD>2, FS<60, MQ>40, MQ Rank Sum >12.5, Read Pos Rank Sum >8.0. Additional filtering retained high-quality variants with parameters: minor allele count=4, max missing=0.20, min q=30, min-mean DP=6, max mean DP=60, minDP=6, max DP=60.
   Quantities: Final dataset: 335 individuals, 768,339 high-quality SNPsDuration: Not specifiedConditions: GATK v4.0 pipeline with specified quality parameters
   Equipment: fastp, bwa mem, GATK v4.0, VCFtools

Typical Equipment

• fastp
• bwa mem
• GATK v4.0
• VCFtools

Output Measurements

• high-quality SNP dataset

Papers Using This Protocol (1)

Species Studied With This Protocol