User: mylons

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mylons130
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130
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Location:
Boston, MA
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4 years, 6 months ago
Joined:
9 years, 3 months ago
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m******@gmail.com

computer engineer working in bioinformatics

Posts by mylons

<prev • 18 results • page 1 of 2 • next >
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Forum: Bay Area Community?
... Hey fellow San Francisco and bay area people! I just relocated from Boston, and there were a few bioinformatics meetup groups out there. I was curious if there was something similar here, or just bio-tech computational biology gatherings of any kind? If not, perhaps we should take this opportunity t ...
forum written 7.0 years ago by mylons130
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Minor Allele Frequency Nucleotide In Dbsnp?
... I have a vcf of dbsnp-137, and it occasionally has a GMAF info field with an allele frequency. What I don't understand is how to know which allele, ref or alt, is the minor? I've been looking at several of these by hand via ncbi, and want to know how NBCI is determining that the T is the minor allel ...
allele dbsnp written 7.3 years ago by mylons130 • updated 7.3 years ago by Jorge Amigo11k
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Comment: C: Vcftools Runs Of Homozygosity Option
... what's your command line look like? I can't seem to get any output data using "vcftools --vcf sorted.vcf --LROH --chr chr1" ...
written 7.3 years ago by mylons130
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Comment: C: Can You Please Tell Me Where I Find Information About .Fai File Format?
... Is there a way to do this with picard or GATK itself? I'd love to stay away from samtools if I could. ...
written 7.9 years ago by mylons130
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Comment: C: Dbsnp Rod File Still Useful?
... Yes it did. I also finally found this documentation on the portion I was about to use: http://www.broadinstitute.org/gsa/gatkdocs/release/orgbroadinstitutestinggatkwalkersindelsRealignerTargetCreator.html They state this in there: --known / -known (List[RodBinding[VariantContext]] with default va ...
written 7.9 years ago by mylons130
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Dbsnp Rod File Still Useful?
... I've been trying to find the documentation on generating a dbSNP.rod file that used to be in the GATK's re-aligning workflows and documented in the GATK wiki, but due to their new licensing they've taken that site down. I also stumbled upon this, http://jianyingli18.wordpress.com/2011/04/04/gatk- ...
gatk dbsnp written 7.9 years ago by mylons130 • updated 7.9 years ago by Liye Zhang80
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Answer: A: Vcftools In Java, Particularly Vcf-Compare
... This might be worth looking at: https://github.com/broadgsa/gatk/blob/master/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java ...
written 8.0 years ago by mylons130
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Comment: C: Vcftools In Java, Particularly Vcf-Compare
... picard has no support for VCF. GATK does though, and here's a decent example showing how to use it to diff 2 files: https://github.com/broadgsa/gatk/blob/master/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java https://github.com/broadgsa/gatk ...
written 8.0 years ago by mylons130
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Comment: C: Bam : Extract Only Alignment With A Specific Length
... Love the scala use in bioinformatics. Wish it was more prevalent! ...
written 8.0 years ago by mylons130
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Comment: C: Assembly Of 454 Reads From Metagenomic
... What's your estimated coverage of the target genome? Generally, high coverage yields better assemblies ...
written 8.4 years ago by mylons130

Latest awards to mylons

Appreciated 7.0 years ago, created a post with more than 5 votes. For A: Mapping Paired End Solid Data Using Bwa
Popular Question 7.0 years ago, created a question with more than 1,000 views. For Minor Allele Frequency Nucleotide In Dbsnp?
Popular Question 7.0 years ago, created a question with more than 1,000 views. For Dbsnp Rod File Still Useful?
Teacher 7.0 years ago, created an answer with at least 3 up-votes. For A: Mapping Paired End Solid Data Using Bwa

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