2.3 | Read mapping and SNP calling
High-quality reads were aligned to the P. univalens reference
genome (WormBase accession ID: GCA_002259215.1) using BWA-MEM
(0.7.13-r1126)(H. Li & Durbin, 2010) with default parameters. SAMtools
(v0.1.19) (H. Li et al., 2009) was used to convert mapping results into
the BAM format and filtered the unmapped and non-unique mapping reads.
The Parascaris equorum reference genome (WormBase project ID:
PRJEB514) was used for species identification. Duplicated reads were
marked with the Picard Tools (picard.sourceforge.net, Version: 2.1.1).
Then Genome Analysis Toolkit (GATK v 4.0.3.0) (Depristo, Banks, Poplin,
Garimella, & Daly, 2011) were used to population SNP calling. Then hard
filtering was applied to the raw variant set using ”QD < 2.0
|| FS > 60.0 || MQ
< 20.0 || MQRankSum < -12.5
|| ReadPosRankSum < -8.0” –filter-name
”snp_filter”. SNPs with >1% missing data or
<0.01 minor allele frequency (MAF) were filtered out using
vcftools (v0.1.12a) (Danecek et al., 2011) for downstream bioinformatic
analyses. Variants Annotation of variantswere performed according to the
reference genome using the package ANNOVAR (Version: 2015-12-14). Using
the SAMtools software, the coverage of each sample was counted based on
aligned BAM data.