User: Vivek

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Vivek1.9k
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Posts by Vivek

<prev • 225 results • page 1 of 23 • next >
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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 3 months ago by Vivek1.9k
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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 3 months ago by Vivek1.9k
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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 3 months ago by Vivek1.9k
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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 3 months ago by Vivek1.9k
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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 3 months ago by Vivek1.9k
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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 4 months ago by Vivek1.9k
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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 4 months ago by Vivek1.9k
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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 4 months ago by Vivek1.9k
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Comment: C: How to plot coverage and depth statistics of a bam file
... You cannot assume that, some exome capture designs also cover UTR regions. You need to ideally get a specific bed file of targeted regions or alteast the name of the capture kit used so you can go to their webpage and download target regions from there. ...
written 4 months ago by Vivek1.9k
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Comment: C: How to plot coverage and depth statistics of a bam file
... So did you check if the zero coverage positions lie within your targeted regions? If they don't, you can safely exclude them, if they do lie in your target regions and there is a large chunk of them you can ask your sequencing provider about the poor quality. ...
written 4 months ago by Vivek1.9k

Latest awards to Vivek

Good Question 14 days ago, asked a question that was upvoted at least 5 times. For Identifying De Novo Variants In Trio Data
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: data science courses, offered by John Hopkins University at Coursera
Great Question 6 weeks ago, created a question with more than 5,000 views. For Identifying De Novo Variants In Trio Data
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: VCF files: Change Chromosome Notation
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: VCF files: Change Chromosome Notation
Appreciated 3 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 8 months ago, created a question with more than 1,000 views. For 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Appreciated 9 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 9 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
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Appreciated 12 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 12 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Scholar 14 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Appreciated 17 months ago, created a post with more than 5 votes. For A: VCF files: Change Chromosome Notation
Popular Question 18 months ago, created a question with more than 1,000 views. For Variant Present In 1000 Genomes Data But Not In Esp
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 22 months ago, created a question with more than 1,000 views. For Vep Not Giving Annotation With Refseq Transcript

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