你的命令行写错了吧，你检查检查的；
gatk call SNP样品多采取方法2，报错如下是怎么回事啊
A USER ERROR has occurred: Argument emit-ref-confidence has a bad value: Can only be used in single sample mode currently. Use the --sample-name argument to run on a single sample out of a multi-sample BAM file
用的是这个 for i in bk-c-a1 bk-c-a2 bk-c-a3 bk-x-a1 bk-x-a2 bk-x-a3; do echo "RUN CMD: gatk --java-options '-Xmx4g' HaplotypeCaller -R $REF \ -I $workdir/3.map/result/${i}.sorted.dedup.bam \ -O ${i}.g.vcf.gz --max-alternate-alleles 4 --sample-ploidy 2 \ -ERC GVCF --tmp-dir $tmpdir" gatk --java-options "-Xmx4g" HaplotypeCaller -R $REF \ -I $workdir/3.map/result/${i}.sorted.dedup.bam \ -O ${i}.g.vcf.gz --max-alternate-alleles 4 --sample-ploidy 2 \ -ERC GVCF --tmp-dir $tmpdir done
重新 提交问题吧，看不清