User: Robert Sicko

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Robert Sicko610
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Posts by Robert Sicko

<prev • 86 results • page 1 of 9 • next >
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Comment: C: NGS Data Storage Best Practices (Clinical)
... 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 7 months ago by Robert Sicko610
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Comment: C: NGS Data Storage Best Practices (Clinical)
... 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 7 months ago by Robert Sicko610
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Forum: NGS Data Storage Best Practices (Clinical)
... 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 ...
ngs forum clinical storage written 7 months ago by Robert Sicko610 • updated 7 months ago by genomax87k
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Comment: C: How to create a tab delimited file?
... I haven't seen this command before. Awesome! ...
written 17 months ago by Robert Sicko610
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Comment: C: Calling CFTR Poly TG/Poly T Genotype
... 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 17 months ago by Robert Sicko610
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Comment: C: Calling CFTR Poly TG/Poly T Genotype
... 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 17 months ago by Robert Sicko610
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Answer: A: Calling CFTR Poly TG/Poly T Genotype
... 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 17 months ago by Robert Sicko610
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Calling CFTR Poly TG/Poly T Genotype
... 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 ...
ngs alignment written 18 months ago by Robert Sicko610 • updated 17 months ago by Charles Warden7.8k
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Comment: C: Estimating cross contamination in a set of BAMS
... **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 2.1 years ago by Robert Sicko610
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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 2.6 years ago by Robert Sicko610

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For BWA mem alignment taking a while in a virtual machine
Epic Question 6 months ago, created a question with more than 10,000 views. For Renaming All Files In A Directory With A Perl Script
Scholar 10 months ago, created an answer that has been accepted. For A: Question in Database of Genomic variants
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Question in Database of Genomic variants
Scholar 17 months ago, created an answer that has been accepted. For A: Question in Database of Genomic variants
Popular Question 19 months ago, created a question with more than 1,000 views. For Functional annotation of network of gene-sets
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Popular Question 23 months ago, created a question with more than 1,000 views. For Functional annotation of network of gene-sets
Popular Question 2.1 years ago, created a question with more than 1,000 views. For BWA mem alignment taking a while in a virtual machine
Scholar 2.7 years ago, created an answer that has been accepted. For A: Question in Database of Genomic variants
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Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Do You Want Your Exome/Genome Sequenced?
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Question in Database of Genomic variants
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Calculating Depth For Each Amplicon From A Mapped Bam
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Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Question in Database of Genomic variants
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Performing Pathway Analysis On Cnv Data
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Popular Question 5.5 years ago, created a question with more than 1,000 views. For Calculating Depth For Each Amplicon From A Mapped Bam
Scholar 5.6 years ago, created an answer that has been accepted. For A: Question in Database of Genomic variants
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Do You Want Your Exome/Genome Sequenced?
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Renaming All Files In A Directory With A Perl Script

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