User: devenvyas

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devenvyas570
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570
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Location:
Stony Brook
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1 year, 1 month ago
Joined:
4 years, 10 months ago
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Posts by devenvyas

<prev • 191 results • page 1 of 20 • next >
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When did SNP genotyping arrays first come into use in research?
... This isn't exactly a bioinformatics question, but it is something I have been wondering and this is a community where people commonly use array data. When did SNP genotyping arrays first come into use in research (particularly in human research)? ...
snp written 22 months ago by devenvyas570 • updated 22 months ago by Petr Ponomarenko2.6k
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How I do lift over a Plink bim file from Hg18 to Hg19.
... I've got some very old SNP data from Data Dryad. The BIM files uses coordinates from Hg18, but my dataset uses coordinates from Hg19. I was wondering if anyone knows how to liftover coordinates in a Plink BIM file? ...
plink snp written 22 months ago by devenvyas570 • updated 21 months ago by ml.endale0
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Answer: A: ANNOVAR is losing 886 SNPs, and I can't figure out why
... So I figured out how to do this. I am writing it up as an answer, so future users can refer to it if they have the same problem Basically, I identified 886 SNPs, which were monomorphic in my dataset (and thus getting lost in the VCF to avinput conversion). I created a bim file for the 886 SNPs and ...
written 23 months ago by devenvyas570
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Comment: C: ANNOVAR is losing 886 SNPs, and I can't figure out why
... Then something might be getting lost when Plink converts from bed/bim/fam to VCF. The bim file clears displays both alleles (even though the derived allele is absent for 886 sites). I created a bim for just those 886 sites, and I reformatted it to avinput format and cat'ed it to the end of actual a ...
written 23 months ago by devenvyas570
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Comment: C: ANNOVAR is losing 886 SNPs, and I can't figure out why
... Within Plink, all the samples are monomorphic, so ANNOVAR ignores them instead of including them in the avinput file Unless I add more samples that have the derived versions of those SNPs, ANNOVAR will think they are monomorphic and ignore them. There must be some way to override this. ...
written 23 months ago by devenvyas570
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Answer: A: How to call mitochondrial SNP?
... This may not be as helpful, but have you tried to use Mapping-Iterative-Assembler, you can just assemble whole mitochondrial genomes and then align to the rCRS and call SNPs that way ...
written 23 months ago by devenvyas570
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Comment: C: ANNOVAR is losing 886 SNPs, and I can't figure out why
... It appears that there are 886 that are completely monomorphic within my dataset, so ANNOVAR is ignoring them instead of including them... Here are five examples rs377583051 rs561224271 rs544889745 rs573338017 rs555351100 ...
written 23 months ago by devenvyas570
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ANNOVAR is losing 886 SNPs, and I can't figure out why
... I have a SNP dataset in Plink for 419,102 SNPs. I am trying to run them through ANNOVAR, so I can figure out what types of functional elements they are spread in across the genome. plink --bfile input --recode vcf-iid --out Ancestral_419k convert2annovar.pl -format vcf4old Ancestral_419k.v ...
snp written 23 months ago by devenvyas570
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Need help plotting D statistics
... I am trying to generate a figure that looks like the third/bottom portion of this figure (where there are French/Sardinian as Y and others as X) http://www.nature.com/nature/journal/v514/n7523/fig_tab/nature13810_F3.html I know I need to use ggplot2 to generate these but I don't have an idea how. I ...
R written 23 months ago by devenvyas570
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Comment: C: Where can I upload SNP array data for public accessibility?
... It's still bioinformatics, so it is still relevant here. From what I have noticed, most of the time the data gets put on the PIs website, but my advisor is wary of doing that. I am guessing unless someone else has any other suggestions, DataDryad is probably the place. ...
written 2.4 years ago by devenvyas570

Latest awards to devenvyas

Popular Question 20 months ago, created a question with more than 1,000 views. For Good way to graph allele frequency of different SNPs along chromosomes
Popular Question 20 months ago, created a question with more than 1,000 views. For How to obtain ancestral alleles based on Hg19 genome coordinates?
Popular Question 20 months ago, created a question with more than 1,000 views. For VCFtools not filtering VCF file by positions
Popular Question 20 months ago, created a question with more than 1,000 views. For What is a bad lowest-CV value for Admixture?
Popular Question 20 months ago, created a question with more than 1,000 views. For Set uniform bar widths for ADMIXTURE barplots in R
Popular Question 20 months ago, created a question with more than 1,000 views. For Setting dimensions of barplot area in R (for STRUCTURE-like plot)
Popular Question 20 months ago, created a question with more than 1,000 views. For [SOLVED] Two Plink map/ped files refuse to merge.
Popular Question 20 months ago, created a question with more than 1,000 views. For Need help transposing MAP file and PED file into one large table
Popular Question 21 months ago, created a question with more than 1,000 views. For How to obtain ancestral alleles based on Hg19 genome coordinates?
Popular Question 21 months ago, created a question with more than 1,000 views. For VCFtools not filtering VCF file by positions
Popular Question 21 months ago, created a question with more than 1,000 views. For Set uniform bar widths for ADMIXTURE barplots in R
Popular Question 21 months ago, created a question with more than 1,000 views. For Setting dimensions of barplot area in R (for STRUCTURE-like plot)
Popular Question 22 months ago, created a question with more than 1,000 views. For How to obtain ancestral alleles based on Hg19 genome coordinates?
Popular Question 22 months ago, created a question with more than 1,000 views. For VCFtools not filtering VCF file by positions
Popular Question 22 months ago, created a question with more than 1,000 views. For Setting dimensions of barplot area in R (for STRUCTURE-like plot)
Popular Question 22 months ago, created a question with more than 1,000 views. For [SOLVED] Two Plink map/ped files refuse to merge.
Popular Question 23 months ago, created a question with more than 1,000 views. For VCFtools not filtering VCF file by positions
Scholar 23 months ago, created an answer that has been accepted. For A: What is a bad GATK Genotype Quality?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For VCFtools not filtering VCF file by positions
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Setting dimensions of barplot area in R (for STRUCTURE-like plot)
Popular Question 2.1 years ago, created a question with more than 1,000 views. For [SOLVED] Two Plink map/ped files refuse to merge.
Great Question 2.3 years ago, created a question with more than 5,000 views. For What are good settings for filtering VCF files?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Setting dimensions of barplot area in R (for STRUCTURE-like plot)
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Just got back raw Affy Axiom SNP data from core lab, where do I start? (new learner)

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