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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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strange biostar214299 results #209

Closed seven1112233 closed 1 year ago

seven1112233 commented 1 year ago

Hi! I want to find reads with special variants(such as: chr1:2000- C to T mutation) by using biostar214299. After snps calling with bam fileA, I got some variants(such as: chr1:2000- C to T mutation) , but when I use biostar214299 to find reads with those variants(format: chr1 2000 T sites1) in bam fileA, I just got 1 read return. I guess something wrong happen. could you tell me about biostar214299 whether it works for paired-end reads?

lindenb commented 1 year ago

@seven1112233 Thank you for the bug report. I haven't used this tool for years. Can you please join a small bam file containing the reads overlapping the position ?

seven1112233 commented 1 year ago

Thank you for your reply!  I have found out the way to solved this and your tools is very helpful to me!

------------------ 原始邮件 ------------------ 发件人: "lindenb/jvarkit" @.>; 发送时间: 2022年9月14日(星期三) 凌晨3:01 @.>; @.**@.>; 主题: Re: [lindenb/jvarkit] strange biostar214299 results (Issue #209)

@seven1112233 Thank you for the bug report. I haven't used this tool for years. Can you please join a small bam file containing the reads overlapping the position ?

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