User: devenvyas

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devenvyas620
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Stony Brook
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Posts by devenvyas

<prev • 199 results • page 1 of 20 • next >
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Recs for what to use for analyzing IBS sharing (from phased, imputed VCFs)?
... I have imputed GZ.VCFs from Beagle 4.0 based on some ancient DNA VCFs (24 individuals). Beagle phased the genotypes in their output. I am looking to do some IBD tract sharing analyses between 24 samples. Does anyone have recommendations on what software package to use for the imputation? ...
ibd written 29 days ago by devenvyas620
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Comment: C: Clipping reads within BAM files?
... I do have the FASTQs. Adapters were trimmed. The idea here is to uniformly clip additional bases to make sure the damaged bases are removed. We are not quite sure what is causing the batch effect. It could be quality score related. There is a lot more variation in the partially UDG set than in the ...
written 3 months ago by devenvyas620
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Finding number of reads and base calls at ~10,000 non-SNPs using BAM file?
... I am working on paleogenomic data. I have BAM files from two different datasets that were processed/sequenced different. I am trying to look into some relationships between post-mortem damage and batch effects. I have BAM files for each individual. I have ~10,000 sites where are monomorphic to refe ...
bam ancientdna written 3 months ago by devenvyas620
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Clipping reads within BAM files?
... I am on paleogenomic data. I have BAM files from two different datasets that were processed/sequenced different (one was partially UDG treated, one was not UDG treated at all - the latter was sequenced on a newer machine). Most of my comparisons between the two datasets are plagued by batch effects ...
bam written 3 months ago by devenvyas620 • updated 3 months ago by manuel.belmadani1.2k
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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 7 months ago by devenvyas620
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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 8 months ago by devenvyas620
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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 months ago by devenvyas620
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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 10 months ago by devenvyas620 • updated 9 months 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 2.8 years ago by devenvyas620 • updated 2.8 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 2.8 years ago by devenvyas620 • updated 10 weeks ago by Shicheng Guo8.0k

Latest awards to devenvyas

Popular Question 3 months ago, created a question with more than 1,000 views. For Is there a way to filter Plink files based off a cluster file
Great Question 3 months ago, created a question with more than 5,000 views. For Coding genotypes from nucleotides to 0/1/2 in R.
Popular Question 7 months ago, created a question with more than 1,000 views. For Is there a way to filter Plink files based off a cluster file
Popular Question 7 months ago, created a question with more than 1,000 views. For Filtering a VCF based on Map Quality
Popular Question 7 months ago, created a question with more than 1,000 views. For Good way of plotting a statistic with error bars
Popular Question 7 months ago, created a question with more than 1,000 views. For Setting two outgroups in Treemix
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Good way to graph allele frequency of different SNPs along chromosomes
Popular Question 7 months ago, created a question with more than 1,000 views. For Does Treemix support multithreaded analyses?
Great Question 7 months ago, created a question with more than 5,000 views. For Coding genotypes from nucleotides to 0/1/2 in R.
Popular Question 8 months ago, created a question with more than 1,000 views. For Setting two outgroups in Treemix
Popular Question 8 months ago, created a question with more than 1,000 views. For Good way of plotting a statistic with error bars
Popular Question 9 months ago, created a question with more than 1,000 views. For Filtering a VCF based on Map Quality
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to obtain ancestral alleles based on Hg19 genome coordinates?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Filtering down 1000 Genomes data just for a set of SNPs
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Creating a tree from pairwise FST values for ADMIXTURE components
Epic Question 2.1 years ago, created a question with more than 10,000 views. For What are good settings for filtering VCF files?
Epic Question 2.1 years ago, created a question with more than 10,000 views. For Filtering a vcf file with vcftools, where is my output?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Filtering a VCF based on Map Quality
Good Question 2.1 years ago, asked a question that was upvoted at least 5 times. For What are good settings for filtering VCF files?
Great Question 2.1 years ago, created a question with more than 5,000 views. For Filtering a vcf file with vcftools, where is my output?
Appreciated 2.1 years ago, created a post with more than 5 votes. For What are good settings for filtering VCF files?

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