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tassel 報錯 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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1 個回答

omicsgene - 生物信息
擅長:重測序,遺傳進化,轉錄組,GWAS

排下序就行,用排好序的文件再輸入即可避免錯誤:

#利用tassel軟件對文件進行排序
run_pipeline.pl?-Xmx30G??-SortGenotypeFilePlugin?-inputFile?clean.vcf.gz?\
????-outputFile?clean.sorted.vcf.gz?-fileType?VCF

#vcf文件格式轉換成Phylip格式,用于后續構建進化樹
run_pipeline.pl??-Xmx5G?-importGuess??$workdir/00.filter/clean.sorted.vcf.gz??\
????-ExportPlugin?-saveAs?supergene.phy?-format?Phylip_Inter
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