snpdat: GBS data from Shirasawa et al (2017)

In updog: Flexible Genotyping for Polyploids

GBS data from Shirasawa et al (2017)

Description

Contains counts of reference alleles and total read counts from the GBS data of Shirasawa et al (2017) for the three SNPs used as examples in Gerard et. al. (2018).

Usage

snpdat

Format

A tibble with 419 rows and 4 columns:

id

The identification label of the individuals.

snp

The SNP label.

counts

The number of read-counts that support the reference allele.

size

The total number of read-counts at a given SNP.

Value

A tibble. See the Format Section.

Source

\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/srep44207")}

References

• Shirasawa, Kenta, Masaru Tanaka, Yasuhiro Takahata, Daifu Ma, Qinghe Cao, Qingchang Liu, Hong Zhai, Sang-Soo Kwak, Jae Cheol Jeong, Ung-Han Yoon, Hyeong-Un Lee, Hideki Hirakawa, and Sahiko Isobe "A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)." Scientific Reports 7 (2017). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/srep44207")}

• Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping Polyploids from Messy Sequencing Data. Genetics, 210(3), 789-807. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/genetics.118.301468")}.

updog documentation built on May 29, 2024, 8:13 a.m.