User: vigprasud

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vigprasud60
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60
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United States
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10 months ago
Joined:
5 years, 7 months ago
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Posts by vigprasud

<prev • 30 results • page 1 of 3 • next >
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Plotting ROC curve for categorical variables
... I have results from a manual exercise and an automated exercise to predict pathogenicity of variants. How do I show an ROC that shows FP rate and the performance of the tool ? `Variant Predicted Reported` `2:17959282:C:T LikelyPathogenic Likely Pathogenic` `2:17961268:C:T LikelyPathogenic ...
genetics roccurve regression written 10 months ago by vigprasud60
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Comment: C: Splice prediction from bam files
... DNA-seq bams ...
written 23 months ago by vigprasud60
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Splice prediction from bam files
... Are there any command line tools that specialize in predicting splice site variants from bams? ...
splicesite wes written 23 months ago by vigprasud60 • updated 23 months ago by WouterDeCoster33k
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How to get gemini to display only the column headers of a database
... How do I get gemini to print only the column headers of a database?  Thanks in advance! ...
gemini pedigree variantframework written 3.2 years ago by vigprasud60 • updated 3.2 years ago by karl.stamm3.3k
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(Closed) alternative for mget with ability to resume download upon connection termination
... I am trying to transfer files from a remote server to my machine using smbclient. I am using mget to get all the files. But mget does not perform incremental/resumable downloads, so any network-level errors that occur during transfer will result in an incomplete and/or corrupt output. Is there an eq ...
mget filetransfer linux smbclient written 3.3 years ago by vigprasud60
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Comment: C: VCF genotype generator
... I am trying to find a simulator software not a variant caller given bams [unlike a GGA call].  ...
written 3.4 years ago by vigprasud60
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VCF genotype generator
... Does someone know of a software that can simulate genotypes for a variant with AC and AN counts, given a set of variants? I am assuming AC will help generate the heterozygous variants [0/1] or homozygous [1/1] and AN can give the number of samples needed in a VCF format.      ...
vcf ngs genotypes written 3.4 years ago by vigprasud60 • updated 3.3 years ago by Len Trigg1.2k
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tabix a text file
... Is there a way to tabix a text file and use it for quick retrieval of records? I have these fields in a text file  #CHR START STOP GENE I would like to retrieve the records based on chr:start-pos.    My sample file [sample.txt] has this data chr1    11873   14361   A chr1    14469   29370   B ...
tabix text written 3.6 years ago by vigprasud60 • updated 23 months ago by Biostar ♦♦ 20
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Comment: C: Mapping fastq files with paired reads and member of the paired reads not present
... I tried the script. I got the pairs seperate but I could not get them in order.  R1.fq has  ReadA/1 ReadB/1 ReadC/1  while R2.fq has ReadC/2 ReadA/2 ReadB/2   Is there a way that this program sorts them ?? ...
written 4.0 years ago by vigprasud60
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Comment: C: Mapping fastq files with paired reads and member of the paired reads not present
... Thanks, The singles are combined or are they printed out in different files as well? ...
written 4.0 years ago by vigprasud60

Latest awards to vigprasud

Popular Question 22 months ago, created a question with more than 1,000 views. For VCF genotype generator
Popular Question 22 months ago, created a question with more than 1,000 views. For Looking For Snp'S That Are Significantly Differentially Expressed
Popular Question 23 months ago, created a question with more than 1,000 views. For Looking For Snp'S That Are Significantly Differentially Expressed
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Looking For Snp'S That Are Significantly Differentially Expressed
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Retrieve mutation position and ID for a mutation in hgvs format
Student 3.0 years ago, asked a question with at least 3 up-votes. For ClinVar Mutation representations and Descriptions
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Trying to Understand why and how NGS Reads follow Poisson Distribution
Popular Question 3.1 years ago, created a question with more than 1,000 views. For ClinVar Mutation representations and Descriptions
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Trying to Understand why and how NGS Reads follow Poisson Distribution
Supporter 4.3 years ago, voted at least 25 times.

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