User: Robert Sicko
Robert Sicko • 570
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Posts by Robert Sicko
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... I haven't seen this command before. Awesome! ...
written 11 weeks ago by
Robert Sicko • 570
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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 12 weeks ago by
Robert Sicko • 570
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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 12 weeks ago by
Robert Sicko • 570
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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 12 weeks ago by
Robert Sicko • 570
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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 3 months ago by
Robert Sicko • 570
• updated
12 weeks ago by
Charles Warden ♦ 6.6k
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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 11 months ago by
Robert Sicko • 570
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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 17 months ago by
Robert Sicko • 570
1
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1
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... Thanks Kevin for pointing me in right direction. I was able to accomplish what I need doing exactly what you say.
For anyone who may run across a similar problem. I used ````bedtools unionbedg```` to output a combined per-base file with depth of each replicate in columns 4 and 5. Then I could ````a ...
written 18 months ago by
Robert Sicko • 570
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... thanks, I figured I was over complicating things. Comparing the per-base output to find the common regions under 20x does seem like a better approach. I'll have to guess and check on finding the regions in common in the per-base output that are under 20x. My initial thought is combine the replicate ...
written 18 months ago by
Robert Sicko • 570
2
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1
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706
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1
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... I'm trying to identify regions of a targeted NGS panel that lack 20x coverage. I've figured out how to get my desired output (described below) per sequencing run. I'm running into trouble figuring out how to use sample replicates and only output regions that are missing in both replicates.
Example: ...
written 18 months ago by
Robert Sicko • 570
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12 weeks ago,
created an answer that has been accepted.
For A: Question in Database of Genomic variants
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For Functional annotation of network of gene-sets
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For Functional annotation of network of gene-sets
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For Functional annotation of network of gene-sets
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For BWA mem alignment taking a while in a virtual machine
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18 months ago,
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For A: Question in Database of Genomic variants
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For BWA mem alignment taking a while in a virtual machine
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For A: Do You Want Your Exome/Genome Sequenced?
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For A: Question in Database of Genomic variants
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For Calculating Depth For Each Amplicon From A Mapped Bam
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For Renaming All Files In A Directory With A Perl Script
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For Calculating Depth For Each Amplicon From A Mapped Bam
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For A: Do You Want Your Exome/Genome Sequenced?
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For A: Question in Database of Genomic variants
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For Renaming All Files In A Directory With A Perl Script
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For A: Do You Want Your Exome/Genome Sequenced?
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For A: Do You Want Your Exome/Genome Sequenced?
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