User: devenvyas

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devenvyas580
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580
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Location:
Stony Brook
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1 week, 3 days ago
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5 years, 2 months ago
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Posts by devenvyas

<prev • 195 results • page 1 of 20 • next >
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How do I get PyVCF to give me an error if the record it is fetching doesn't exist?
... I have a Python script that is supposed to be reading some emit-all VCF files and outputting a transposed Plink file for biallelic sites. The VCFs were called using custom in-house callers and thus are slightly out of spec (since they are ancient DNA), so standard programs like vcftools or bcftools ...
vcf written 10 days ago by devenvyas580
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PCA on pairwise allele sharing counts
... I have a table with pairwise doubleton allele sharing counts, and I am trying to run a PCA on my results Example Sample1 Sample2 Sample3 Sample4 Sample5 Sample1 - 7 13 4 13 Sample2 7 - 2 15 8 Sample3 13 2 - 11 10 Sample4 4 15 11 - 5 Sample5 13 8 10 5 - Each value in ...
pca snp written 4 weeks ago by devenvyas580
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Reorienting 1000 Genome VCF files, so that derived alleles are always ALT
... Hello, I am working with the 1000 Genomes Project phase 3 VCF files. I am trying to figure out how to reorient the REF and ALT alleles so that the derived allele is always the ALT. I tried the --derived option in vcftools, but that apparently does nothing for the VCF output files. ...
vcf snp written 9 weeks ago by devenvyas580
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Constructing a Y chromosome phylogeny from VCF files
... I have <34 VCF files for the 9.9Mb callable NRY bases per Poznik et al. 2013 (10.1126/science.1237619). (One individual per VCF, some are from women, so they will be omitted) I want to construct a phylogeny/network to study how they differ. Does anyone have a recommended method/pipeline? ...
vcf phylogeny written 12 weeks ago by devenvyas580 • updated 10 weeks ago by sankar200410
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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 2.2 years ago by devenvyas580 • updated 2.2 years 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 2.2 years ago by devenvyas580 • updated 2.1 years 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 2.2 years ago by devenvyas580
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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 2.2 years ago by devenvyas580
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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 2.2 years ago by devenvyas580
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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 2.2 years ago by devenvyas580

Latest awards to devenvyas

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Setting two outgroups in Treemix
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Popular Question 17 months ago, created a question with more than 1,000 views. For Filtering a VCF based on Map Quality
Good Question 17 months ago, asked a question that was upvoted at least 5 times. For What are good settings for filtering VCF files?
Great Question 17 months ago, created a question with more than 5,000 views. For Filtering a vcf file with vcftools, where is my output?
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Appreciated 17 months ago, created a post with more than 5 votes. For What are good settings for filtering VCF files?

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