Reference allele mismatch at chr1:1630781 .. REF_SEQ:'C' vs VCF:'T' Ref alleles mismatch between: [VC Unknown @ chr1:1630781 Q. of type=SNP alleles=[T*, C] attr={} GT=[[HG00472 T*/C]] ..

原因是待处理的vcf,他们的ref allele不一致，所以

解决方法是 bcftools norm  先统一 ref allele

如bcftools norm -c s -f /ldfssz1/ST_BIGDATA/USER/st_bigdata/Sentieon/reference_bigdatacompute/hg38_noalt_withrandom/hg38.fa -o /jdfssz1/ST_HEALTH/P21Z10200N0047/lizhichao/zbolt_test/data_input/1Kgenome/microarray_vcf/ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.1_22.sort.vcf.reheaderzbolt.reref.gz -O z /jdfssz1/ST_HEALTH/P21Z10200N0047/lizhichao/zbolt_test/data_input/1Kgenome/microarray_vcf/ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.1_22.sort.vcf.reheaderzbolt.gz && echo "re_ref done"

 

参数：-c s 很重要。