User: Robert Sicko
Robert Sicko • 590
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Posts by Robert Sicko
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... True, I edited my comment for clarity. Yes, we would only be saving the fastqs if we needed to variant call with an updated pipeline or something similar. Most of the reasons we've seen/I can think of for reprocessing from bcl files (sample sheet error, process failure during fastq generation) would ...
written 3 months ago by
Robert Sicko • 590
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... Our director has advised storing fastqs in case we need to rerun downstream analysis etc, but she was OK with removing raw data after 2-3 months.
We are a screening lab, so we're in a weird space of not technically being a diagnostic lab but we're using molecular tests and validating more NGS that ...
written 3 months ago by
Robert Sicko • 590
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... I'm in a lab that does clinical and research NGS and we have daily clinical MiSeq runs. I want to start purging raw MiSeq results to save space.
We know we want to retain raw data for awhile.I'm unsure if I should just create a script that copies the fastqs to an archive directory or a script that ...
written 3 months ago by
Robert Sicko • 590
• updated
3 months ago by
genomax ♦ 80k
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... I haven't seen this command before. Awesome! ...
written 13 months ago by
Robert Sicko • 590
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... Charles, I looked into GET-evidence further. I see their about page does at least states it is not clinical quality:
> "GET-Evidence is not a “clinical quality” tool for diagnosis or
> treatment of any disease or medical condition."
They do allow anyone with a login to [edit][1] their annot ...
written 13 months ago by
Robert Sicko • 590
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... Charles, thank you for the thoughtful response. I completely agree with your statement on the need to throughly validate variant calling, especially in a targeted panel, especially when reporting clinically. We are validating the assay for clinical use (screening). The script I posted above is only ...
written 13 months ago by
Robert Sicko • 590
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... Just to wrap this up. I found this [paper][1]. I contacted Dr. Pagin and he explained their script used grep on fastqs and counted different alleles to make a call per sample. I used that idea in this [script][2]. If anyone uses this script in the future, the HET_CUTOFF (line 554) will likely vary d ...
written 13 months ago by
Robert Sicko • 590
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... Background: The CFTR gene has a Poly TG/Poly T region in intron 8 that has [varying clinical][1] consequences.
I'm using targeted NGS for this region (150bp, paried end) and I'm trying to call the PolyTG/PolyT genotypes from fastq files. My first attempt was bbmap run with default parameters and a ...
written 14 months ago by
Robert Sicko • 590
• updated
13 months ago by
Charles Warden ♦ 7.6k
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... **verifyBamID** does need a vcf, but it is a population reference VCF (1000genomes)
I've used it for detecting contamination in a targeted panel with alright results. see my [question][1] on their user group page.
reference_vcf=/media/sf_BigShare/SCID/180213_TSCA_r1_sop_test/work/reference/180 ...
written 21 months ago by
Robert Sicko • 590
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Comment:
C: BWA mem running extremely slow
... Any chance you can allocate more memory? I'm guessing your 14Gbp reference will require just over 24gigs.
I [had 5gig allocated for human genome][1] and alignment was really slow. After I followed Heng's advice and ran with 6gig it was normal speed.
3.1 human reference/5.5 gig minimum allocation = ...
written 2.3 years ago by
Robert Sicko • 590
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