User: Vivek

gravatar for Vivek
Vivek1.9k
Reputation:
1,880
Status:
Trusted
Location:
Denmark
Scholar ID:
Google Scholar Page
Last seen:
6 hours ago
Joined:
5 years, 2 months ago
Email:
a**************@gmail.com

Bioinformatics Developer

Posts by Vivek

<prev • 225 results • page 1 of 23 • next >
0
votes
2
answers
197
views
2
answers
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 5 weeks ago by Vivek1.9k
1
vote
2
answers
327
views
2
answers
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 weeks ago by Vivek1.9k
2
votes
1
answer
183
views
1
answers
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 weeks ago by Vivek1.9k
2
votes
2
answers
327
views
2
answers
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 7 weeks ago by Vivek1.9k
6
votes
2
answers
327
views
2
answers
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 7 weeks ago by Vivek1.9k
1
vote
5
answers
22k
views
5
answers
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 8 weeks ago by Vivek1.9k
2
votes
5
answers
22k
views
5
answers
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 8 weeks ago by Vivek1.9k
0
votes
1
answer
144
views
1
answers
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 9 weeks ago by Vivek1.9k
1
vote
5
answers
22k
views
5
answers
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 11 weeks ago by Vivek1.9k
1
vote
5
answers
22k
views
5
answers
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 11 weeks ago by Vivek1.9k

Latest awards to Vivek

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: VCF files: Change Chromosome Notation
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 7 weeks ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 6 months ago, created a question with more than 1,000 views. For 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Appreciated 6 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 7 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Scholar 8 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Appreciated 10 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 10 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Scholar 12 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Appreciated 15 months ago, created a post with more than 5 votes. For A: VCF files: Change Chromosome Notation
Popular Question 15 months ago, created a question with more than 1,000 views. For Variant Present In 1000 Genomes Data But Not In Esp
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 19 months ago, created a question with more than 1,000 views. For Vep Not Giving Annotation With Refseq Transcript
Popular Question 20 months ago, created a question with more than 1,000 views. For ClinVar download sources
Popular Question 22 months ago, created a question with more than 1,000 views. For Vep Not Giving Annotation With Refseq Transcript
Student 2.1 years ago, asked a question with at least 3 up-votes. For Identifying De Novo Variants In Trio Data
Scholar 2.2 years ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Tabix Perl Api Examples

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1842 users visited in the last hour