[GangSTR-2.5.0] ERROR: Error extracting read length

[jackzhong1995]

Dear all,

I got the error "[GangSTR-2.5.0] ERROR: Error extracting read length" when I run GangSTR. I try to found solution but noway.

First, I make sure the reference matches what my bam file is aligned to (version and annotation, i.e., chrX vs X). Then I only remain all the reads with length=150bp using the command: "samtools view -h my.bam | awk 'length($10) == 150 || $1~/^@/' | samtools view -b -@ 2 -o my.cl.bam -" Finally, I still got the error: "Error extracting read length"

What should I do? I'm looking forward to your reply. Best wishes.

[jackzhong1995]

I'm sorry, no

来自阿里邮箱Android客户端------------------------------------------------------------------ @.> 日　期：2024年01月08日 16:42:13 @.> @.>; @.> 主　题：Re: [gymreklab/GangSTR] [GangSTR-2.5.0] ERROR: Error extracting read length (Issue #122)

Have you successfully solved this problem? I also encountered this error when using the bam files generated by bwa mem, but the bam files generated by bwa aln work fine. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>