multiple processing with single .bam file gonna make problems??
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6 months ago
hs960201 ▴ 10

hi

i'm just doing my first WGS analysis (cancer). so, i wanna do some variant calling process with my BWA aligned, sorted, duplicates removed .bam files such as Varscan2, Delly... something like that.

so i'm doing Strelka2 processing right now for SNVs calling. my question is..

is it OK to run other process (Delly for SV calling) with bam files that already being processed?

servers CPU and RAM is enough to processing but all my fear is, what if multiple tools make catastrophic events and ruin my processed .bam file

i'm new to BI and Linux programming for my master degree... although my question looks silly (probably it is)

please. help me

thanks

WGS strelka2 squenza varscan2 file processing • 211 views
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6 months ago
anfor ▴ 10

hi, Work on copy or have a look at data versioning systems like pins (R package) ... best A

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6 months ago
GenoMax 101k

is it OK to run other process (Delly for SV calling) with bam files that already being processed?

It should be ok to work on a file (read) with multiple programs as long as you have storage/hardware infrastructure that is robust and performant. You obviously don't want to write to the same file handle from multiple programs. That would be bad.

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