Tutorial:Genotype And Snp Calling Review Papers

Question

[Istvan Albert]

Review papers on the topic of genoype and snp calling.

DNA sequencing

• SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data (April 2012) in PLoS ONE
• Genotype and SNP calling from next-generation sequencing data (June 2011) in Nature Reviews Genetics
• Pacific biosciences sequencing technology for genotyping and variation discovery in human data (2012) BMC Genomics 2012,

Bisulfite sequencing

• Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data (July 2012) in Genome Biology

Biostar posts tagged as

• snp+snpcalling
• dbsnp

Back to the Table of Contents

Answer 1

[NextGenSeek]

Pacific biosciences sequencing technology for genotyping and variation discovery in human data, Mauricio O Carneiro, Carsten Russ, Michael G Ross, Stacey Gabriel, Chad Nusbaum and Mark A DePristo, BMC Genomics 2012, 13:375

Answer 2

[willgilks]

Sequencing 200 individual Drosophila. Identified SNPs, indels and CNVs up to 100Kb. Data, code, qc graphs, summaries and logs are released:

Gilks WP, Pennell TM, Flis I et al. Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample. F1000Research 2016, 5:2644 (doi: 10.12688/f1000research.9912.3)