DOI: 10.5061/dryad.2fqz612w5
title: RecView: An interactive R application for locating recombination positions using pedigree data

description: We present RecView, an interactive R application and its homonymous R
 package, to facilitate locating recombination positions along chromosomes
 or scaffolds using whole-genome genotype data of a three-generation
 pedigree. We demonstrate applicability of RecView using the genotype data
 from two offspring, as well as their grandparents and parents, of the
 great reed warbler (Acrocephalus arundinaceus).
description: We randomly selected a
 three-generation pedigree, including 4 grandparents (Aarun_H7-38,
 Aarun_H0-81, Aarun_V9-73, Aarun_H7-41), 2 parents (Aarun_H3-00,
 Aarun_H5-17) and 2 offspring (ID-256 and ID-258), from our long-term study
 population of great reed warblers at Lake Kvismaren, southern Central
 Sweden (59°10ʹ N, 15°24ʹ E). The birds were whole-genome sequenced with
 Illumina. The sequence reads were trimmed,
 mapped to the great reed
 warbler genome assembly, and read duplicates were
 removed. Then, a VCF file
 of called variants were produced, and the genotypes at bi-allelic SNPs on
 chromosome 1 and 21 were extracted. In addition to the full dataset, we downsampled
 the number of SNPs to 10% and 1% of the original number (referred to as
 the “10% downsampled dataset” and “1% downsampled
 dataset”).
description: # Description of the files The dataset is from a three-generation pedigree
 of great reed warbler (*Acrocephalus arundinaceus*) including 4
 grandparents (Aarun_H7-38, Aarun_H0-81, Aarun_V9-73, Aarun_H7-41), 2
 parents (Aarun_H3-00, Aarun_H5-17) and 2 offspring (ID-256 and ID-258). ##
 1 VCF files VCF files consist of bi-allelic SNPs on chromosome 1 and 21 of
 the great reed warbler. ### 1.1 VCF files list * full_dataset.vcf.gz:
 bi-allelic SNPs on chromosome 1 and 21, referred to as full dataset. *
 10percent_downsampled_dataset.vcf.gz: 10% downsampling of the total number
 of bi-allelic SNPs on chromosome 1 and 21 from the full dataset. *
 1percent_downsampled_dataset.vcf.gz: 1% downsampling of the total number
 of bi-allelic SNPs on chromosome 1 and 21 from the full dataset. ### 1.2
 Variable explanation * CHROM: The column contains the labels of scaffolds
 in the great reed warbler reference genome acrAru1 (BioProject ID
 PRJNA765537). * POS: The column contains the positions on the scaffolds
 for the bi-allelic SNPs. * Aarun_H7-38: Aarun_H7-38 is the label for the
 paternal grandfather at F0 generation of the three-generation pedigree.
 The column contains the FORMAT information of VCF file (see headings in
 VCF files for details) for this individual. * Aarun_H0-81: Aarun_H0-81 is
 the label for the paternal grandmother at F0 generation of the
 three-generation pedigree. The column contains the FORMAT information of
 VCF file (see headings in VCF files for details) for this individual. *
 Aarun_V9-73: Aarun_V9-73 is the label for the maternal grandfather at F0
 generation of the three-generation pedigree. The column contains the
 FORMAT information of VCF file (see headings in VCF files for details) for
 this individual. * Aarun_H7-41: Aarun_H7-41 is the label for the maternal
 grandmother at F0 generation of the three-generation pedigree. The column
 contains the FORMAT information of VCF file (see headings in VCF files for
 details) for this individual. * Aarun_H3-00: Aarun_H3-00 is the label for
 the father at F1 generation of the three-generation pedigree. The column
 contains the FORMAT information of VCF file (see headings in VCF files for
 details) for this individual. * Aarun_H5-17: Aarun_H5-17 is the label for
 the mother at F1 generation of the three-generation pedigree. The column
 contains the FORMAT information of VCF file (see headings in VCF files for
 details) for this individual. * ID-256: ID-256 is the label for the
 offspring at F2 generation of the three-generation pedigree. The column
 contains the FORMAT information of VCF file (see headings in VCF files for
 details) for this individual. * ID-258: ID-258 is the label for the
 offspring at F2 generation of the three-generation pedigree. The column
 contains the FORMAT information of VCF file (see headings in VCF files for
 details) for this individual. ## 2 Genotype files Genotype files consist
 of unphased genotypes extracted from the VCF files using vcftools option:
 --extract-FORMAT-info GT. ### 2.1 Genotype files list * full_dataset.GT:
 genotypes extracted from the full_dataset.vcf.gz. *
 10percent_downsampled_dataset.GT: genotypes extracted from
 10percent_downsampled_dataset.vcf.gz. * 1percent_downsampled_dataset.GT:
 genotypes extracted from 1percent_downsampled_dataset.vcf.gz. ### 2.2
 Variable explanation * CHROM: The column contains the labels of scaffolds
 in the great reed warbler reference genome acrAru1 (BioProject ID
 PRJNA765537). * POS: The column contains the positions on the scaffolds
 for the bi-allelic SNPs. * Aarun_H7-38: Aarun_H7-38 is the label for the
 paternal grandfather at F0 generation of the three-generation pedigree.
 The column contains genotypes at bi-allelic SNPs for this individual. *
 Aarun_H0-81: Aarun_H0-81 is the label for the paternal grandmother at F0
 generation of the three-generation pedigree. The column contains genotypes
 at bi-allelic SNPs for this individual. * Aarun_V9-73: Aarun_V9-73 is the
 label for the maternal grandfather at F0 generation of the
 three-generation pedigree. The column contains genotypes at bi-allelic
 SNPs for this individual. * Aarun_H7-41: Aarun_H7-41 is the label for the
 maternal grandmother at F0 generation of the three-generation pedigree.
 The column contains genotypes at bi-allelic SNPs for this individual. *
 Aarun_H3-00: Aarun_H3-00 is the label for the father at F1 generation of
 the three-generation pedigree. The column contains genotypes at bi-allelic
 SNPs for this individual. * Aarun_H5-17: Aarun_H5-17 is the label for the
 mother at F1 generation of the three-generation pedigree. The column
 contains genotypes at bi-allelic SNPs for this individual. * ID-256:
 ID-256 is the label for the offspring at F2 generation of the
 three-generation pedigree. The column contains genotypes at bi-allelic
 SNPs for this individual. * ID-258: ID-258 is the label for the offspring
 at F2 generation of the three-generation pedigree. The column contains
 genotypes at bi-allelic SNPs for this individual. ## 3 Scaffold file
 Scaffold file consists of the order and orientation information of the
 scaffolds on chromosome 1 and 21. ### 3.1 Scaffold file list *
 scaffold_file.csv: the order and orientation information of the scaffolds
 on chromosome 1 and 21 extracted from great reed warbler reference genome
 acrAru1 (BioProject ID PRJNA765537). ### 3.2 Variable explanation *
 scaffold: The column contains the labels of scaffolds in the great reed
 warbler reference genome acrAru1 (BioProject ID PRJNA765537). * size: The
 column contains the size in base pairs for the scaffolds. * CHR: The
 column contains the chromosomal assignment for the scaffolds in great reed
 warbler. * order: The column contains the order of the scaffolds on each
 chromosome. * orientaion: The column contains the orientaion of the
 scaffolds on each chromosome.