Beagle填充The first genotype is diploid, but the genotype at position NW_024599719.1:207426 is haploid

 

001、Beagle填充报错：The first genotype is diploid, but the genotype at position NW_024599719.1:207426 is haploid

 

002、使用命令

java -Xmx160g \-jar /public/home/b20223040323/software/beagle/beagle.27Feb25.75f.jar \nthreads=16 \gt=plink_vcf.vcf \out=NW_dir_114_impute

 

003、根据日志定位原因

从原始的VCF文件中提取报错个体SRR12235035的VCF文件：

bcftools view -s SRR12235035 -Oz -o SRR12235035.vcf.gz NW_dir_114_snp_filter_geno09maf001.vcf

 

004、提取SRR12235035个体的207426位置的基因型

grep -v "^#" SRR12235035.vcf | grep "NW_024599719" | grep 207426

 这个位点实际上是缺失的位点，推测可能是Beagle并不能识别造成的报错。

 

005、解决方法，使用plink转换为VCF

plink --vcf NW_dir_114_snp_filter_geno09maf001.vcf --allow-extra-chr --double-id --recode vcf-iid --out plink_vcf

再次phasing和填充。