User: vivekruhela

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vivekruhela10
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Posts by vivekruhela

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Simple count of dbSNP (rs...) from .vcf file
... Please write it as an answer and close it so that others can easily find it and get help from. Thanks for providing better solution. ...
written 6 weeks ago by vivekruhela10
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Comment: C: filtering pindel results
... Hi, Actually, I don't get it. In my pindel output file, I also got numerous entries. If I try your way, then I got 16,824 entries out of 1,44,563. Definitely, it is very less as compared to original one. But there are many 0/0 which are either INS or DEL, then how can I remove them. What will you ...
written 8 weeks ago by vivekruhela10
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Information about control data
... Hi, I am putting this question because I did not find any useful information from internet because of limited access. My question is related to control (or normal) data that we use for somatic mutation detection (with the help of mutect or SomaticSnipper etc) with tumor data. Here are the questions ...
genome next-gen sequence sequencing written 10 weeks ago by vivekruhela10
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Comment: C: How to combine multiple tools to detct SVs in WES data
... Sorry I have again one more question: Is it ok to combine two gVCF files. One from Haplotype and another from Unifiedgenotype. I think it may be ok because both are complete files (i.e. consensus call) contains record from each position. So can we do this. Thanks. ...
written 10 weeks ago by vivekruhela10
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Comment: C: How to determine high-quality somatic mutations
... Hey, sorry for very late response again. The link sent by you for nature paper, author has used controlled data but the difference is author has used control data of difference patient and tumor data of different and then used optimization technique for fitness function stabilization. And that contr ...
written 11 weeks ago by vivekruhela10
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How to get unique somatic mutations for each individual patients
... Hi, I apologize if it is too simple question but I got stuck here. Here is the situation: I have exome data 32 patients. My aim is to identify unique somatic mutations in each patients. For this I have completed my pipeline for Whole Exome Data analysis using various tools like BWA mem, picard, ga ...
gene R next-gen sequence snp written 11 weeks ago by vivekruhela10
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Comment: C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
... I have a doubt in the command suggested by you. `-f` stands for only taking those reads. So if you have written `-f 0x02` that means reads associated with all other flags will be discarded and only `0x02` associated reads will be considered. Then there is no need of mentioning those flag whose assoc ...
written 11 weeks ago by vivekruhela10
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Comment: C: Percentage of uniquely mapped reads
... Thanks. I'll check it. ...
written 11 weeks ago by vivekruhela10
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Comment: C: should I merge fastq files for different lanes before do QC?
... So you mean to say that it is OK to merge `S1_L001_R1_001.fastq` and `S1_L002_R1_001.fastq` because both are forward. Or I should do merging of `S1_L001_R1_001.fastq` (forward) and `S1_L001_R2_001.fastq` (reverse). I need your suggestions. I also want to know about cluster based analysis of fastq fi ...
written 11 weeks ago by vivekruhela10
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Comment: C: Converting Gvcf Files Into Vcf
... I tried running the file `get_called_regions`, I am getting nothing means 0kb file as ab output...I have checked it and repeat it many times still I ma not getting any output. Need some suggestions..and please add proper documentation also. Thanks ...
written 11 weeks ago by vivekruhela10

Latest awards to vivekruhela

Supporter 11 weeks ago, voted at least 25 times.
Scholar 3 months ago, created an answer that has been accepted. For A: How to combine multiple tools to detct SVs in WES data

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