User: devenvyas

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devenvyas650
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Stony Brook
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1 month ago
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Posts by devenvyas

<prev • 204 results • page 1 of 21 • next >
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How do I convert GPs to GLs?
... I want to run NgsAdmix on a set of imputed data. The data was imputed through Beagle and thus has GPs. NgsAdmix takes input beagle files that are derived from GL/PL data (`vcftools --vcf input.vcf --out test --BEAGLE-GL --chr 1,2`) How do I convert GPs into GLs (or PLs), so I can use them? http:// ...
vcf imputation written 4 weeks ago by devenvyas650
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Imputing missing genetic map distances from a bim file
... I have a Plink dataset with 7.1 millions biallelic SNPs (which are in 1000G phase 3). I was able to recover genetic map distances for 2.5 million, but not for the rest. I was wondering, is there a way I can get Plink or any other piece of software to impute the missing map distances? ...
plink snp centimorgan written 5 months ago by devenvyas650 • updated 7 days ago by shenzhongjun0
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Getting centimorgan map units for 1000 Genomes data
... I have imputed VCFs, which I imputed using Beagle for 1000G reference sites (http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/). From these, I have a bed/bim/fam file that I made using plink19 --vcf FILENAME --make-bed --out. The resulting bim file has no map units, which I n ...
plink written 5 months ago by devenvyas650 • updated 5 months ago by Kevin Blighe65k
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Comment: C: Plot local ancestry on chromosome
... Did you ever find a solution? The Martin approach hard limits to three reference populations. ...
written 6 months ago by devenvyas650
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How do I plot RFMix results?
... I am running RFMix to identify ancestry segments on each of the 22 autosomes. I have seen these types of results in human genetics/anthropological genetics papers/talks, where you have the 22 pairs of chromosomes and segments are colored to represent the individual's relation to different reference ...
R written 6 months ago by devenvyas650 • updated 5 months ago by Biostar ♦♦ 20
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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 8 months ago by devenvyas650
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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 10 months ago by devenvyas650
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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 10 months ago by devenvyas650
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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 10 months ago by devenvyas650 • updated 10 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 14 months ago by devenvyas650

Latest awards to devenvyas

Popular Question 6 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
Student 8 months ago, asked a question with at least 3 up-votes. For Filtering a vcf file with vcftools, where is my output?
Great Question 10 months ago, created a question with more than 5,000 views. For Coding genotypes from nucleotides to 0/1/2 in R.
Popular Question 10 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
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Good way to graph allele frequency of different SNPs along chromosomes
Great Question 14 months ago, created a question with more than 5,000 views. For Coding genotypes from nucleotides to 0/1/2 in R.
Popular Question 14 months ago, created a question with more than 1,000 views. For Setting two outgroups in Treemix
Popular Question 14 months ago, created a question with more than 1,000 views. For Good way of plotting a statistic with error bars
Popular Question 14 months ago, created a question with more than 1,000 views. For Filtering a VCF based on Map Quality
Popular Question 14 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 14 months ago, created a question with more than 1,000 views. For Does Treemix support multithreaded analyses?
Popular Question 15 months ago, created a question with more than 1,000 views. For Setting two outgroups in Treemix
Popular Question 15 months ago, created a question with more than 1,000 views. For Good way of plotting a statistic with error bars
Popular Question 16 months ago, created a question with more than 1,000 views. For Filtering a VCF based on Map Quality
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Filtering a VCF based on Map Quality
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Creating a tree from pairwise FST values for ADMIXTURE components
Epic Question 2.7 years ago, created a question with more than 10,000 views. For What are good settings for filtering VCF files?
Epic Question 2.7 years ago, created a question with more than 10,000 views. For Filtering a vcf file with vcftools, where is my output?
Good Question 2.7 years ago, asked a question that was upvoted at least 5 times. For What are good settings for filtering VCF files?
Great Question 2.7 years ago, created a question with more than 5,000 views. For Filtering a vcf file with vcftools, where is my output?
Appreciated 2.7 years ago, created a post with more than 5 votes. For What are good settings for filtering VCF files?

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