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Missing pair end parameters:bamfile, histo_file, mean, stdev, read_length, min_non_overlap, discordant_z #393

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psardana22 opened this issue Feb 8, 2024 · 0 comments

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@psardana22
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Hi lumpy team,
I have been working on running lumpy to call large structural variants. I have been running lumpy traditional where I generated insert size distributions following the below command.
samtools view -r readgroup1 sample.bam
| tail -n+100000
| scripts/pairend_distro.py
-r 101
-X 4
-N 10000
-o sample.lib1.histo
However, after this when I try running the lumpy , it shows me missing pair end parameters even after mentioning the parameters.
Could you please help? I am attaching the snippet of the code that I have written.
Looking forward to hearing from you
Lumpy-error

Thanks and regards,
Prachi

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