User: Vivek

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Vivek2.0k
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Bioinformatics Developer

Posts by Vivek

<prev • 227 results • page 1 of 23 • next >
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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 2 days ago by Vivek2.0k
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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 4 weeks ago by Vivek2.0k
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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 6 months ago by Vivek2.0k
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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 6 months ago by Vivek2.0k
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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 6 months ago by Vivek2.0k
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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 6 months ago by Vivek2.0k
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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 6 months ago by Vivek2.0k
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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 7 months ago by Vivek2.0k
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Comment: C: How to plot coverage and depth statistics of a bam file
... I'd assume ref.core.targets_merged.bed is a subset of ref_plus_utr.targets.bed. If so that is the file you should use, if not merge the files together using BEDtools merge and use the resulting bed file. You can ignore the baits bed files. ...
written 7 months ago by Vivek2.0k
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Answer: A: Mapping ORFs to Chromosome locations
... You can align the sequences using BLAT. https://genome.ucsc.edu/cgi-bin/hgBlat?command=start Convert the top alignments from the resulting PSL file to BED format and use BEDtools to check the intersection with your coordinates. ...
written 7 months ago by Vivek2.0k

Latest awards to Vivek

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For Identifying De Novo Variants In Trio Data
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
Great Question 4 months ago, created a question with more than 5,000 views. For Identifying De Novo Variants In Trio Data
Popular Question 4 months ago, created a question with more than 1,000 views. For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: VCF files: Change Chromosome Notation
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: VCF files: Change Chromosome Notation
Appreciated 6 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 6 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 11 months ago, created a question with more than 1,000 views. For 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Appreciated 12 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 13 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
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Appreciated 15 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 15 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Scholar 18 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Appreciated 20 months ago, created a post with more than 5 votes. For A: VCF files: Change Chromosome Notation
Popular Question 21 months ago, created a question with more than 1,000 views. For Variant Present In 1000 Genomes Data But Not In Esp
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates

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