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Using basecounts, is there a way to output read name list containing indels on a specific chromosome position? #2

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YingziZhang-github opened this issue Mar 1, 2023 · 0 comments

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@YingziZhang-github
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Hi,

Thank you very much for developing basecounts tool.

As the issue title describes, I need to obtain a read name list (or read fastq file) containing indels on a specific chromosome position. Could basecounts give such output?

To clarify, I want to exclude reads with only SNVs but not indels on the chromosome position. However, the tools I have found till now (e.g., ASCIIGenome) can only find reads containing SNVs and indels as a pool, but cannot separate reads containing SNVs and reads containing indels.

Many thanks.
Yingzi

@YingziZhang-github YingziZhang-github changed the title Using basecounts, is there a way to output read name list containing indels on a certain chromosome position? Using basecounts, is there a way to output read name list containing indels on a specific chromosome position? Mar 1, 2023
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