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starskyzheng / panpop

Application of pan-genome for population
MIT License
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long_caller_parser.pl会删除几乎所有的DEL？ #65

Closed hui-liu closed 1 week ago

hui-liu commented 1 month ago

用最新版的Sniffles2（v2.4）得到SV后，使用long_caller_parser.pl进行过滤，发现几乎所有的DEL都被删除，请问这是什么原因？

starskyzheng commented 1 month ago

请列举一个被删掉的DEL，把vcf的那一行贴出来看看

hui-liu commented 1 month ago

例如： 1 349925 Sniffles2.DEL.FE5S0 CGTTTCTGAAAGGCCCCGATCCGGACTGCCTAAAGTCCGGTCGAGAGAAGTCCTAGCCAACGATCCTATTGAGGATCGCGGGCGTTACA C 60 PASS PRECISE;SVTYPE=DEL;SVLEN=-88;END=350013;SUPPORT=38;COVERAGE=40,39,39,39,36;STRAND=+-;AF=0.974;STDEV_LEN=0.740;STDEV_POS=0.655 GT:GQ:DR:DV 1/1:60:1:38

starskyzheng commented 1 month ago

看起来没啥问题，源文件方便上传么？我重现一下试试

hui-liu commented 1 month ago

这是VCF文件： ERR11436632.vcf.gz

参考基因组是拟南芥：https://www.arabidopsis.org/download/file?path=Sequences/Assemblies/TAIR9_chr_all.fas

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