NGS文章阅读: Whole-genome resequenci

变异检测软件部分 Variant detection

First, we used the index function from BWA v0.7.17 to construct a reference genome Sus scrofa 11.1.

Then, alignment was performed using the mem algorithm from BWA and sorted binary bam files were obtained via SAMtools v1.9

Several functions from Sentieon software were used to detect variants:

1. LocusCollectora and Realigner functions were used to remove duplicate reads and realigned indels;
2. the QualCal function was used to perform Base Quality Score Recalibration;
3. the Haplotyper method was used to generate gvcf files, and the GVCFtyper function was used to perform joint calling.

Thereafter, hard filtering was implemented under the criteria of QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < −12.5 || ReadPosRankSum < −8.0 || SOR > 3.0 via the VariantFiltration method from GATK v4.0.2.1 .

Finally, a total of 30,987,305 SNPs with minor allele frequency > 0.01 and call rate > 0.9 were obtained using PLINK v1.9 .