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GATK variant calling (Pieridae)

Subcategory: genomic analysis
Papers: 1 | Mentions: 1

Local Knowledge Graph (35 entities)

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Knowledge graph centered on GATK variant calling (Pieridae) with 35 nodes and 117 connections. Top connected: Ligusticum porteri, Atriplex canescens, Lepidoptera, Populus, Boechera stricta.

Description

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

Typical Equipment

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

Output Measurements

  • high-quality SNP dataset

Papers Using This Protocol (1)

article

Patterns of genetic variation and local adaptation of a native herbivore to a lethal invasive plant

2024Molecular Ecologyusing

Species Studied With This Protocol

Cardamine cordifolia

Brassicaceae1 paper

Populus

Salicaceae1 paper

Thlaspi arvense

Brassicaceae1 paper

Lepidoptera

1 paper

Atriplex canescens

not mentioned1 paper

Hereford

1 paper

native species

1 paper

non-native plants

1 paper

non-native species

1 paper

Thlaspi

Brassicaceae1 paper