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Variant calling against pig reference genome (GCA_000003025.6) using pig strain reads

ABSTRACT: We ran nf-core/sarek pipeline using 297 paired-end reads from 130 samples from 15 different pig strains. 5 callers were utilised - strelka, deepvariant, freebayes, haplotypecaller, and mpileup. Variants were retained if called by at least 3 callers. The genotyping was done on strelka and deepvariant gVCF output using illumina gvcfgenotyper and GLnexus respectively. The best genotype is retained based on genotype quality. The pipeline generated ~15 million novel variants that would enrich variant deserts on the pig reference genome.

INSTRUMENT(S): -

ORGANISM(S): Sus Scrofa

SUBMITTER: EMBL-EBI

PROVIDER: PRJEB93975 | EVA | 2025-07-19

REPOSITORIES: EVA

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Dataset's files

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			Action	DRS
	pig_gca000003025v6_calls_with_strains.cohort.1.qc.accessioned.vcf.gz	Vcf
	pig_gca000003025v6_calls_with_strains.cohort.1.qc.accessioned.vcf.gz.csi	Vcf
	pig_gca000003025v6_calls_with_strains.cohort.1.qc.vcf.csi	Other
	pig_gca000003025v6_calls_with_strains.cohort.1.qc.vcf.gz	Vcf
	pig_gca000003025v6_calls_with_strains.cohort.10.qc.accessioned.vcf.gz	Vcf

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