tassel 报错 SortGenotypeFilePlugin to correctly order the file.

ERROR net.maizegenetics.plugindef.AbstractPlugin - Problem loading file: /work/my_pop_cucu/00.filter/clean.vcf.gz. Error: BuilderFromVCF: Ordering incorrect. VCF file must be ordered by position. Please first use SortGenotypeFilePlugin to correctly order the file.

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分类：GWAS

默认排序时间排序

2 个回答

omicsgene - 生物信息 2022-04-28 09:22

擅长：重测序,遗传进化,转录组,GWAS

排下序就行，用排好序的文件再输入即可避免错误：

#利用tassel软件对文件进行排序
run_pipeline.pl -Xmx30G  -SortGenotypeFilePlugin -inputFile clean.vcf.gz \
    -outputFile clean.sorted.vcf.gz -fileType VCF

#vcf文件格式转换成Phylip格式，用于后续构建进化树
run_pipeline.pl  -Xmx5G -importGuess  $workdir/00.filter/clean.sorted.vcf.gz  \
    -ExportPlugin -saveAs supergene.phy -format Phylip_Inter

Marina 2024-04-25 17:50

你好，在用水稻3k数据库的ped去跑plink的时候，遇到了这样的报错：

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - BuilderFromPLINK: build: problem processing: / by zero

tassel 报错 SortGenotypeFilePlugin to correctly order the file.

2 个回答

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