cnv

[Ashesltz]

why i usually get invalid mutation 'All reads is filtered in this scope, total & filtered reads num 3716'

[yulijia]

Hi, From the published paper, you can find that the software only deals with 5 types of reads in your target regions, because the reads on your target region don't meet requirements for editing, that why you got all reads were filtered.

[Ashesltz]

could you tell me how to find the target region with 5 types of reads

------------------ 原始邮件 ------------------ 发件人: "nccl-jmli/VarBen" @.>; 发送时间: 2021年12月17日(星期五) 下午2:37 @.>; @.**@.>; 主题: Re: [nccl-jmli/VarBen] cnv (Issue #21)

Hi, From the published paper, you can find that the software only deals with 5 types of reads in your target regions, because the reads on your target region don't meet requirements for editing, that why you got all reads were filtered.

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[yulijia]

I realized that some users may not understand the parameters correctly, there is a parameter -l in sveditor.py, you need to set this value to the read length of input Bam file, otherwise, all reads will be filtered out. Please check the -l parameter in your script.

-l READLENGTH, --readlength READLENGTH read length of bam reads