利用GATK 分染色体call 变异时出现错误

我用如下命令：

for i in $(cat $workdir/data/data.txt) ; do

for Chr in Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 Chr11 Chr12; do

echo "gatk --java-options "-Xmx100g" HaplotypeCaller \

-R $REF \

-I $workdir/3.map/result/${i}.sorted.dedup.bam \

-O ${i}.${Chr}.g.vcf.gz \

--max-alternate-alleles 4 \

--sample-ploidy 2 \

-ERC GVCF \

-L ${Chr} \ # 指定染色体

--tmp-dir $tmpdir"

done

done > gvcf.sh

然后转后台运行 gvcf.sh。出现了以下错误A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ', }' but no positional argument is defined for this tool

0 条评论
分类：重测序

默认排序时间排序

2 个回答

每天学习一点点 1天前

把你的shell脚本截图看一下

omicsgene - 生物信息 1天前

擅长：重测序,遗传进化,转录组,GWAS

bash \ 后面不要有任何字符包括空格；

for i in $(cat $workdir/data/data.txt) ; do 
for Chr in Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 Chr11 Chr12; do
  echo "gatk --java-options "-Xmx100g" HaplotypeCaller \
    -R $REF \
    -I $workdir/3.map/result/${i}.sorted.dedup.bam \
    -O ${i}.${Chr}.g.vcf.gz \
    --max-alternate-alleles 4 \
    --sample-ploidy 2 \
    -ERC GVCF \
    -L ${Chr} \
    --tmp-dir $tmpdir"
done
done > gvcf.sh

利用GATK 分染色体call 变异时出现错误

2 个回答

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