User: jvijai

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jvijai1.1k
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Posts by jvijai

<prev • 81 results • page 1 of 9 • next >
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Comment: C: loading plink format (generated by vcftools) file into Haploview
... Does anyone have a solution for this? It is unclear from the Haploview documentation, what kinda PLINK file should be an input. a PED and MAP converted from VCF via PLINK does not work. I am interested in a solution on this too. ...
written 3.4 years ago by jvijai1.1k
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Answer: A: Mutated Gene Sequence Database For Breast Cancer
... Your HolyGrail is hosted by NHGRI here http://research.nhgri.nih.gov/projects/bic/ ...
written 7.2 years ago by jvijai1.1k
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Comment: C: Gatk Baq And Dbsnp Option In Countvariates
... Your best bet for answers on GATK is here: https://getsatisfaction.com/gsa/topics ...
written 7.2 years ago by jvijai1.1k
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Comment: C: Convert .Map To .Bam
... Did you look at the bowtie tutorial ? http://bowtie-bio.sourceforge.net/tutorial.shtml ...
written 7.3 years ago by jvijai1.1k
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Answer: A: Pairwise Snp Ld Scoring
... You can use SNAP from Broad to get pairwise LD between two SNPs or a list of SNPs. You can also find other SNPs that are in LD (proxySNPs) for your SNPs. You can use specific populations, (different hapmap datasets including 1000genomes). You can also find if those SNPs have membership in major comm ...
written 7.3 years ago by jvijai1.1k
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Designs For Validating Ngs Variants
... I am trying to get a consensus on the best tools used by the community for validation of variants SNVs, Indels that are discovered from NGS (exome or genome). The old fashioned Sanger sequencing is still our current method since we always try to get fast validation of low hanging fruits, which are j ...
vcf bed next-gen primer written 7.3 years ago by jvijai1.1k • updated 7.3 years ago by Pierre Lindenbaum121k
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Answer: A: Mendelian Filter
... You may want to try Var-Sifter from NCI http://research.nhgri.nih.gov/software/VarSifter/ It changes the 1 based coordinates to 2 based coordinates after you read the file in it. So when going back to check predictions etc, you may want to reconvert. The Custom-query section is what you are looking ...
written 7.3 years ago by jvijai1.1k
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Comment: C: Understanding Vcf File Format
... Why does the AD have two values GT:0/1 AD:19,17 DP:36 GQ:87.16 PL483,0,532 ...
written 7.3 years ago by jvijai1.1k
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Comment: C: Vcf-Compare Vcftools Error
... you can start by validating both the VCF files. vcf-validator example.vcf Can you run the other commands such as vcf-stats etc on these files? ...
written 7.4 years ago by jvijai1.1k
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Comment: C: Pairwise Snp Ld Scoring
... http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml#ld2 shows an example of how to do this. Do you have genotype data or just a list of SNPs? If only SNPlist, do you know the ethnicity to use a comparable Hapmap population? ...
written 7.4 years ago by jvijai1.1k

Latest awards to jvijai

Popular Question 4.8 years ago, created a question with more than 1,000 views. For Amino Acid Position In Ucsc Browser
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Query For A List Of Snp Alleles, Frequency Ceu, Strand
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Getting Ucsc Data Via Mysql
Appreciated 6.6 years ago, created a post with more than 5 votes. For A: The Best Question To Ask In A Bioinformatics Seminar
Appreciated 6.6 years ago, created a post with more than 5 votes. For A: How To Convert The Bed File To Ped File
Appreciated 6.6 years ago, created a post with more than 5 votes. For How To Check If The Iupac Snp Code Changes Translation ?
Appreciated 6.6 years ago, created a post with more than 5 votes. For Has Anyone Had Experience With Complete Genomics Sequencing And Data Analysis?
Good Question 6.6 years ago, asked a question that was upvoted at least 5 times. For How To Check If The Iupac Snp Code Changes Translation ?
Good Question 6.6 years ago, asked a question that was upvoted at least 5 times. For Has Anyone Had Experience With Complete Genomics Sequencing And Data Analysis?
Good Answer 6.6 years ago, created an answer that was upvoted at least 5 times. For A: How To Convert The Bed File To Ped File
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Amino Acid Position In Ucsc Browser
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Getting Genes For Snps From Ucsc Browser
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Getting Ucsc Data Via Mysql
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Query For A List Of Snp Alleles, Frequency Ceu, Strand
Popular Question 6.6 years ago, created a question with more than 1,000 views. For How To Check If The Iupac Snp Code Changes Translation ?
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Has Anyone Had Experience With Complete Genomics Sequencing And Data Analysis?
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Gnu Parallel To Perform Illumina Fastq Filter
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Has Anyone Got Plink Working With Gnu Parallel?
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Concordance Of Ngs Data To Wg Snp Array Data
Guru 6.6 years ago, received more than 100 upvotes.
Supporter 6.6 years ago, voted at least 25 times.
Commentator 6.6 years ago, created a comment with at least 3 up-votes. For C: Analysis Of Snps In Gene Deserts
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: Pairwise Snp Ld Scoring
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: Large Genomic Inflation Factor In Gwas
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: Calculating Allele Frequencies From Genotype Data

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