User: Erik Garrison

gravatar for Erik Garrison
Erik Garrison2.2k
Reputation:
2,210
Status:
Trusted
Location:
Napoli, IT / UCSC
Website:
http://hypervolu.me/~e...
Last seen:
1 week, 1 day ago
Joined:
8 years, 12 months ago
Email:
e************@gmail.com

Postdoc at UCSC's Genome Institute, living in Napoli, Italia.

Posts by Erik Garrison

<prev • 77 results • page 1 of 8 • next >
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Comment: C: supporting vg users on biostars
... You caught me as I was doing that. Thanks! I'm just not sure if I should shift the "url" attribute of the repo to point here. It might make it easier to find. ...
written 5 weeks ago by Erik Garrison2.2k
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News: supporting vg users on biostars
... I'd like to announce that we'll be using this forum as a way to provide support to users of [vg](https://github.com/vgteam/vg) and associated tools that work with the same generic data model (a bidirectional DNA sequence graph with paths representing genomes or other important sequences like genes o ...
news vg variation graph graph genome vgteam written 5 weeks ago by Erik Garrison2.2k • updated 5 weeks ago by genomax73k
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Answer: A: Indel Left/Right Alignment
... I suggest taking a look at vt: https://github.com/atks/vt. It includes a very nice left alignment routine. They've got a nice paper describing the method for normalizing the representation: http://bioinformatics.oxfordjournals.org/content/31/13/2202. ...
written 4.0 years ago by Erik Garrison2.2k
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Answer: A: Easy to use local assembly programs ?
... Look no further than Scalpel. I've hacked out the microassembler component of scalpel. It does basically what you're describing except it produces an assembly graph from the BAM file in a particular region. ...
written 4.8 years ago by Erik Garrison2.2k • updated 8 days ago by RamRS24k
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Comment: C: Does The Vcffilter Tool Work On String Type Info Tags?
... So the problem is that you have an integer in your filter, but it's a String type in the file... ...
written 5.1 years ago by Erik Garrison2.2k
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Answer: A: Get Insertion / Deletion Count From Vcf
... vcfstats provides one simple method to do so. You can also generate length-frequency distributions using vcflengthdelta (also in vcflib). ...
written 5.9 years ago by Erik Garrison2.2k
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Comment: C: Gatk - Haplotypecaller Is So Slow, What Is Faster And As Good?
... It ultimately calls and reports point mutations, not haplotypes. The haplotype-based aspect of detection is driven by the debruijn assembly which is used to detect possible alleles. ...
written 5.9 years ago by Erik Garrison2.2k
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Answer: A: Filters/Quality For Vcf Generated By Freebayes
... minimal pipeline and filtering You should get pretty far simply by marking duplicates. You may not need to do this if you didn't use PCR amplification in your library preparation, but it shouldn't hurt. Brad Chapman has worked up a "minimal" pipeline, and he shows that it works basically as well ...
written 5.9 years ago by Erik Garrison2.2k
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Comment: C: What License Do You Use When You Release Code And Data?
... I'm with you both! ...
written 6.0 years ago by Erik Garrison2.2k
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Answer: A: How To Get A List Of All Correlated Snps (In Ld) With Another List Of Snps?
... If you can pull the SNPs out of the 1000 Genomes VCF, you can then run vcf-tools --hap-r2 or something suitable. If the SNPs are close together, you can use the fully-phased VCF and --hap-r2. Otherwise you may need to use --geno-r2, which is probably what you want anyway. Good luck. ...
written 6.0 years ago by Erik Garrison2.2k

Latest awards to Erik Garrison

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Vcf Programming Language Api'S / Parsers Available?
Great Question 4.0 years ago, created a question with more than 5,000 views. For Vcflib Documentation
Scholar 4.0 years ago, created an answer that has been accepted. For A: Easy to use local assembly programs ?
Scholar 4.0 years ago, created an answer that has been accepted. For A: Haloplex & Allele Calling
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Predicting Biologically Significant Snps
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Vcf Programming Language Api'S / Parsers Available?
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Easy to use local assembly programs ?
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Good Answer 4.8 years ago, created an answer that was upvoted at least 5 times. For A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Good Answer 4.8 years ago, created an answer that was upvoted at least 5 times. For A: What Methods Do You Use For In/Del/Snp Calling?
Good Answer 4.8 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Scholar 4.8 years ago, created an answer that has been accepted. For A: Easy to use local assembly programs ?
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Predicting Biologically Significant Snps
Good Answer 5.0 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Good Answer 5.1 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Predicting Biologically Significant Snps
Appreciated 5.1 years ago, created a post with more than 5 votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Vcf Programming Language Api'S / Parsers Available?
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Vcflib Documentation
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Predicting Biologically Significant Snps
Appreciated 5.6 years ago, created a post with more than 5 votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Appreciated 5.6 years ago, created a post with more than 5 votes. For A: What Methods Do You Use For In/Del/Snp Calling?
Appreciated 5.6 years ago, created a post with more than 5 votes. For A: Vcf Programming Language Api'S / Parsers Available?

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