Read mapping and genotyping
Reads obtained from sequencing were trimmed to remove adapter sequences
and bases with Phred quality less than 20 using Cutadapt v. 1.14
(Martin, 2011). Trimmed reads were then
mapped to the publicly available monarch reference genome assembly ,
using BWA-MEM v. 0.7.12 (Li & Durbin,
2009). The resulting alignment files were then sorted using SAMtools v.
1.2 (Li et al. , 2009). Indel
realignment, base recalibration and variant recalibration were performed
using GATK v. 3.8.0 (McKenna et
al. , 2010). Variants were called for each sample using the
Haplotypecaller module in GATK v. 3.8.0 and were then genotyped using
the GenotypeGVCFs module in GATK v. 3.8.0
(McKenna et al. , 2010). High
confidence variants with variant quality score greater than 80 were
selected to recalibrate variant quality scores using VQSR filtering in
GATK v. 3.8.0 (McKenna et al. ,
2010). Indels and variants within the repeat regions of the reference
genome were then removed using Vcftools v. 0.1.15
(Danecek et al. , 2011). One sample
(PL3) with the lowest mapping success and genome-wide depth was removed
prior to downstream analysis. Our bioinformatic pipeline is visualized
in Fig. S1.