SNPs from Black,Green,Pinto,Pink,Red and White abalone

Downloadable File
Organism: 
Haliotis rufescens (Red abalone)
Program, Pipeline Name or Method Name: 
GATK
Program, Pipeline or Method version: 
3.5
Algorithm: 
GATK
Source Name: 
SNPs_BlkGrnPntPnkRedWht_GBE2018.vcf renamed from snphylo.output.filtered.sorted.vcf
Source URI: 
(/work/GIF/severin/Purcell/Abalone/GenomePaper/18_phylosnp) on condo
Time Executed: 
09/24/2018
Materials & Methods (Description and/or Program Settings): 
Raw sequences from ten abalone samples (two from each of five species) were quality checked with FastQC (Andrews 2010). Readswere aligned to the H. rufescens genome assembly using BWA-MEM version 0.7.17 with default parameters (Li 2013). The BAM files were sorted (samtools sort), cleaned (picard CleanSam), marked for duplicates (picard MarkDuplicates with REMOVE_DUPLICATES=true), read groups were added (picard AddOrReplaceReadGroups) and SNP/Indel realignment (GATK RealignerTargetCreator) was performed with Picard Tools 2.4.1 (https://broadinstitute.github.io/picard/) and GATK prior to calling SNPs and InDels with the HaplotypeCaller function in GATK version 3.5 (McKenna 2010). Default parameters were used unless otherwise specified. SNPs were filtered with VCFtools version 0.1.14 (Danecek 2011) using the following parameters (--max-non-ref-af 0.8 --non-ref-af 0.2 --hwe 0.001). The phylogenetic tree in Figure 3 was generated with the filtered SNPs using SNPhylo version 2016-02-04 (Lee et al. 2014) using the maximum likelihood method. SNPhylo applies a filter to reduce SNP redundancy by linkage disequilibrium (-b -B 100). Visualization of Figure 3 was performed in FigTree v1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/).