User: vigprasud
vigprasud • 60
- Reputation:
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- 6 months, 1 week ago
- Joined:
- 5 years, 4 months ago
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Posts by vigprasud
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2
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... 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 ...
written 6 months ago by
vigprasud • 60
0
votes
1
answer
585
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1
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Comment:
C: Splice prediction from bam files
... DNA-seq bams ...
written 19 months ago by
vigprasud • 60
0
votes
1
answer
585
views
1
answer
... Are there any command line tools that specialize in predicting splice site variants from bams? ...
written 19 months ago by
vigprasud • 60
• updated
19 months ago by
WouterDeCoster ♦ 30k
0
votes
1
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672
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1
answer
... How do I get gemini to print only the column headers of a database?
Thanks in advance!
...
written 2.9 years ago by
vigprasud • 60
• updated
2.9 years ago by
karl.stamm ♦ 3.3k
0
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887
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... 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 ...
written 3.0 years ago by
vigprasud • 60
0
votes
2
answers
2.0k
views
2
answers
Comment:
C: VCF genotype generator
... I am trying to find a simulator software not a variant caller given bams [unlike a GGA call].
...
written 3.1 years ago by
vigprasud • 60
0
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2
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2.0k
views
2
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... 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.
...
0
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1
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1.9k
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1
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Comment:
C: tabix a text file
... Thanks! fixed it. and it worked.
...
written 3.3 years ago by
vigprasud • 60
6
votes
1
answer
1.9k
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1
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... 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
...
0
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3
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1.6k
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3
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... 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 3.7 years ago by
vigprasud • 60
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For VCF genotype generator
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For Is there a way to filter Pubmed search based on Citation index of the articles or Is there a way to retrieve an articles's citation index in pubmed
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For Retrieve mutation position and ID for a mutation in hgvs format
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For ClinVar Mutation representations and Descriptions
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