The pipline is sourced from the following paper, please cite it if appropriate.

• Whole-genome sequencing and variants data of 304 indigenous goats from Southwest China
• Journal: Scientific Data, 2025, Under Review.
• Authors: Jipan Zhang, Di Zhou, Rong Yang, Zhengang Guo, Xingzhou Tian, Yongju Zhao

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WGS.pipeline

The main steps, software, and code/parameters used from off-machine data to the VCF file are described below.

(1) Quality control of raw reads

• Software: fastp v0.23.4
• Code: fastp_install_dir/fastp -w 8 -i sample.R1.fq -I sample.R2.fq -o sample.R1.clean.fq -O sample.R2.clean.fq

(2) Mapping reads and sorting the BAM file

• Software: Sentieon v202308
• Code: Sentieon_install_dir/bin/sentieon bwa mem -R "@RG\tID:rg_sample\tSM:sample\tPL:$PL" -t 40 -K 10000000 goat.genome.fa sample.R1.clean.fq sample.R2.clean.fq | util sort -t 40 --sam2bam -o sample.sorted.bam -i -

(3) Mark Duplicates

• Software: Sentieon v202308
• Code: Sentieon_install_dir/bin/sentieon driver -t 40 -i sample-sorted.bam --algo LocusCollector --fun score_info sample.score.txt Sentieon_install_dir/bin/sentieon driver -t 40 -i sample-sorted.bam --algo Dedup --score_info sample.score.txt --metrics sample.dedup_metrics.txt sample.deduped.bam

(4) Sequencing accuracy assessment and alignment statistics (optional)

• Software: Sentieon v202308, PanDepth v2.25, and Samtools v1.13
• Code for calculating reads quality: Sentieon_install_dir/bin/sentieon driver -r goat.genome.fa -t 40 -i sample-sorted.bam
  --algo MeanQualityByCycle sample.mq_metrics.txt
  --algo QualDistribution sample.qd_metrics.txt
  --algo GCBias --summary sample.gc_summary.txt sample.gc_metrics.txt
  --algo AlignmentStat sample.aln_metrics.txt
  --algo BaseDistributionByCycle sample.bd_metrics.txt
  --algo QualityYield sample.qy_metrics.txt
  --algo InsertSizeMetricAlgo sample.is_metrics.txt)
• Code for calculating genome coverage: PanDepth_install_dir/pandepth -i sample.deduped.bam -t 8 -o genome.coverage.stat.txt
• Code for calculating mapping rate: Samtools_install_dir/Samtools flagstat -@40 -i sample.deduped.bam > sample.mapped.stat.txt

(5) Variants calling for each sample

• Software: Sentieon v202308
• Code: Sentieon_install_dir/bin/sentieon driver -r goat.genome.fa -t 40 -i sample.deduped.bam --algo Haplotyper --emit_conf=30 --call_conf=30 --emit_mode gvcf sample.gvcf.vcf.gz

(6) Variant joint calling for all samples

• Software: Sentieon v202308
• Code: GVCF_list=gvcf.gz.list.txt #paths to all gVCF files GVCF_inputs=$(awk '{info=info" -v "$0} END {print info}' $GVCF_list) Sentieon_install_dir/bin/sentieon driver -t 40 -r goat.genome.fa --algo GVCFtyper $GVCF_inputs joint-calling.vcf

(7) Variants extraction and hard filtration

• Software: GATK v4.1.8.1
• Code for SNPs: GATK_install_dir/gatk SelectVariants -R goat.genome.fa -V joint-calling.vcf -O filtered.SNP.vcf
  -select '((QD>=2.0 && MQ>=40.0 && FS<=60.0 && SOR<=3.0) && (QD>=2.0 && MQ<40.0 && FS<=60.0 && SOR<=3.0 || MQRankSum>=-12.5 && ReadPosRankSum>=-8.0) && vc.isSNP())'
• Code for InDels: GATK_install_dir/gatk SelectVariants -R goat.genome.fa -V joint-calling.vcf -O filtered.InDel.vcf
  -select '((QD>=2.0 && FS<=200.0 && SOR<=10.0) && (QD>=2.0 && FS<=200.0 && SOR<=10.0 || ReadPosRankSum>=-20.0) && vc.isIndel())'

(8) Further filtration

• Software: VCFtools v0.1.16
• Code for SNPs: Vcftools_install_dir/vcftools --vcf filtered.SNP.vcf --max-alleles 2 --min-alleles 2 --min-meanDP 5 --max-missing 0.9 --remove-filtered-all --recode --recode-INFO-all --out SNP.vcf
• Code for InDels: Vcftools_install_dir/vcftools --vcf filtered.InDel.vcf --min-meanDP 5 --max-missing 0.9 --remove-filtered-all --recode --recode-INFO-all --out InDel.vcf