bcftools给vcf文件添加染色体长度

 

001、

(smcpp_env) [b20223040323@admin2 x_test]$ ls
Africa.recode.vcf.gz  Africa.recode.vcf.gz.tbi  chr.list  GCF_016772045.2_ARS-UI_Ramb_v3.0_genomic.fna.fai
(smcpp_env) [b20223040323@admin2 x_test]$ bcftools view -h Africa.recode.vcf.gz | grep -i "contig" | head -n 3
##contig=<ID=1>
##contig=<ID=2>
##contig=<ID=3>
(smcpp_env) [b20223040323@admin2 x_test]$ bcftools reheader -f GCF_016772045.2_ARS-UI_Ramb_v3.0_genomic.fna.fai -o Africa.recode.with_length.vcf.gz Africa.recode.vcf.gz
(smcpp_env) [b20223040323@admin2 x_test]$ ls
Africa.recode.vcf.gz      Africa.recode.with_length.vcf.gz  GCF_016772045.2_ARS-UI_Ramb_v3.0_genomic.fna.fai
Africa.recode.vcf.gz.tbi  chr.list
(smcpp_env) [b20223040323@admin2 x_test]$ bcftools view -h Africa.recode.with_length.vcf.gz | grep -i "contig" | head -n 3
##contig=<ID=1,length=278617202>
##contig=<ID=2,length=250202058>
##contig=<ID=3,length=226089100>

 

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