Question: multiple processing with single .bam file gonna make problems??
0
gravatar for hs960201
25 days ago by
hs96020110
Republic of Korea/CHA biotech
hs96020110 wrote:

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

ADD COMMENTlink modified 24 days ago by genomax92k • written 25 days ago by hs96020110
1
gravatar for anfor
24 days ago by
anfor10
France
anfor10 wrote:

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

ADD COMMENTlink written 24 days ago by anfor10
1
gravatar for genomax
24 days ago by
genomax92k
United States
genomax92k wrote:

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.

ADD COMMENTlink modified 24 days ago • written 24 days ago by genomax92k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1252 users visited in the last hour