User: Vivek

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Vivek2.1k
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Bioinformatics Developer

Posts by Vivek

<prev • 229 results • page 1 of 23 • next >
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Comment: C: vcf file processing
... There are more elegant solutions if you can do some scripting but here's a crude workflow: If you have one line per gene in the bed file, you can initially split the BED file into one file per gene like this: split -l 1 Genes.bed Genes- Depending on the number of genes, you might produce a l ...
written 6 weeks ago by Vivek2.1k
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Comment: C: vcf file processing
... Are you trying to extract them into separate files per gene or are you trying to run a burden test or something sophisticated? ...
written 6 weeks ago by Vivek2.1k
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Answer: A: How to generate text file having SNP list from bim file in plink?
... awk '{print $2}' your_file.bim > snplist.txt Would work to give you a SNP list but I don't clearly understand what you are trying to do after that. If you are looking to subset a dataset for individuals you need to specify the individuals you want to keep/remove to PLINK. ...
written 4 months ago by Vivek2.1k
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Answer: A: Individual chromosome SNP VCF
... You could download a subset with tabix for the regions you need. tabix -h ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz '2:39967768-39967768' > dbsnp_2_39967768_39967768.vcf ...
written 5 months ago by Vivek2.1k
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Answer: A: Calculating ethnicity of a sample VCF
... To find the ethnic sub group your sample falls in, you could pick a set of common SNPs (MAF > 5% within each sub-population group) common to your sample and the 1000 genomes data. Do a PCA of the 1000 genomes samples using eigenstrat's smartPCA and project your sample into that pre-computed space ...
written 11 months ago by Vivek2.1k
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Comment: C: retrieving from ExAC in VCF format
... If its in the info fields, you can use GATK's SelectVariants utility. Here are some examples on using JEXL expressions to filter your VCF file: https://gatkforums.broadinstitute.org/gatk/discussion/1255/using-jexl-to-apply-hard-filters-or-select-variants-based-on-annotation-values ...
written 11 months ago by Vivek2.1k
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Answer: A: Hardy Weinberg data from 1000 genomes project
... It should be relatively straightforward to calculate using something like this: You can get the SNPs for your region of interest using Tabix: tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:39967768-39967768 > extracted.vcf ...
written 11 months ago by Vivek2.1k
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Comment: C: retrieving from ExAC in VCF format
... There are tools like vcftools, GATK or bcftools that can achieve this: This thread might be helpful: https://www.biostars.org/p/184950/ ...
written 11 months ago by Vivek2.1k
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Answer: A: retrieving from ExAC in VCF format
... You can use tabix and query directly from the FTP: tabix -h ftp://ftp.broadinstitute.org/pub/ExAC_release/current/ExAC.r0.3.1.sites.vep.vcf.gz 2:39967768-39967768 > exported.vcf ...
written 11 months ago by Vivek2.1k
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Comment: C: How to plot coverage and depth statistics of a bam file
... Anything I can suggest here is a guess and you should be getting more information from the people who sequenced the samples as to how they designed the experiment and which regions they planned to target as part of the exome capture. My intuition with merging the bed files is that it consolidates t ...
written 11 months ago by Vivek2.1k

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Commentator 4 months ago, created a comment with at least 3 up-votes. For C: data science courses, offered by John Hopkins University at Coursera
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For Identifying De Novo Variants In Trio Data
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: data science courses, offered by John Hopkins University at Coursera
Popular Question 9 months ago, created a question with more than 1,000 views. For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
Great Question 9 months ago, created a question with more than 5,000 views. For Identifying De Novo Variants In Trio Data
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: VCF files: Change Chromosome Notation
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: VCF files: Change Chromosome Notation
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Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 16 months ago, created a question with more than 1,000 views. For 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Appreciated 17 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
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Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
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Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates

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