User: Erik Garrison

gravatar for Erik Garrison
Erik Garrison2.0k
Reputation:
1,970
Status:
Trusted
Location:
Somerville, MA
Website:
http://hypervolu.me/~e...
Last seen:
2 years, 1 month ago
Joined:
7 years, 1 month ago
Email:
e************@gmail.com

Researcher in the Marth Lab at Boston College.

Posts by Erik Garrison

<prev • 75 results • page 1 of 8 • next >
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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 2.1 years ago by Erik Garrison2.0k
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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 2.9 years ago by Erik Garrison2.0k
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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 3.2 years ago by Erik Garrison2.0k
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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 4.0 years ago by Erik Garrison2.0k
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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 4.1 years ago by Erik Garrison2.0k
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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 4.1 years ago by Erik Garrison2.0k
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Comment: C: What License Do You Use When You Release Code And Data?
... I'm with you both! ...
written 4.1 years ago by Erik Garrison2.0k
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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 4.1 years ago by Erik Garrison2.0k
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Answer: A: Snp Calling Of Tcga Data Using Samtools
... I've also noticed that samtools' default performance is quite slow. Until the recent development work on samtools catches up and provides suitable defaults, I suggest using freebayes. /shameless plug/ You can call somatic variants in a tumor/normal pair as such: freebayes -f ref.fa --pooled-discr ...
written 4.1 years ago by Erik Garrison2.0k
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Comment: C: Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs D
... You can also use freebayes to call them. Specify --pooled-discrete and --genotype-qualities, call germline/somatic at the same time, and then pass the result through vcfsamplediff (vcflib). ...
written 4.1 years ago by Erik Garrison2.0k

Latest awards to Erik Garrison

Good Answer 2.9 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 2.9 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 2.9 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 2.9 years ago, created an answer that has been accepted. For A: Easy to use local assembly programs ?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Predicting Biologically Significant Snps
Good Answer 3.2 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 3.2 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 3.2 years ago, created an answer with at least 3 up-votes. For A: Predicting Biologically Significant Snps
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Vcf Programming Language Api'S / Parsers Available?
Appreciated 3.5 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 3.5 years ago, created a question with more than 1,000 views. For Vcflib Documentation
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Predicting Biologically Significant Snps
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: What Methods Do You Use For In/Del/Snp Calling?
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Vcf Programming Language Api'S / Parsers Available?
Appreciated 3.7 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?
Appreciated 3.7 years ago, created a post with more than 5 votes. For Vcflib Documentation
Good Answer 3.7 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 3.7 years ago, created an answer that was upvoted at least 5 times. For A: What Methods Do You Use For In/Del/Snp Calling?
Guru 3.7 years ago, received more than 100 upvotes.
Supporter 3.7 years ago, voted at least 25 times.
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: What Methods Do You Use For In/Del/Snp Calling?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Comparing Genotypes In Two Vcf Files

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