User: Adam

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Adam940
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940
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5 months, 3 weeks ago
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6 years, 7 months ago
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Posts by Adam

<prev • 67 results • page 1 of 7 • next >
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Answer: A: Filtering on the minor allele in VCFtools
... vcftools --gzvcf vcf_file --mac 2 --stdout --recode | fgrep -v '#' | wc -l ...
written 17 months ago by Adam940
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Answer: A: 1000 genomes technical data: match exon capture probes to samples
... I suggest you email info@1000genomes.org . They are pretty responsive.  ...
written 2.3 years ago by Adam940
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Answer: A: How to obtain human genotype data from dpSNP ftp?
... The VCF files from dbSNP report only sites, not genotypes. To get genotyping data, perhaps you should use data from the 1000 Genomes Project? ...
written 2.4 years ago by Adam940
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Answer: A: Recombination rate cut off values
... Rather than thinking in terms of haploblocks or recombination rate, you might want to think in terms of genetic distance. For example, you might decide to only consider variants within, say, 0.5 cM. In terms of physical distance, this threshold would correspond to approximately 500kb on average, but ...
written 2.5 years ago by Adam940
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Answer: A: 1000G high coverage depth of sequencing?
... They're at least 30X, but can average a bit higher. See the link below (which can be quite slow) for an example.  http://bam.iobio.io/?bam=http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/high_coverage_alignment/HG00096.wgs.ILLUMINA.bwa.GBR.high_cov_pcr_free.20140203.bam&region=1 ...
written 2.5 years ago by Adam940
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Comment: C: Vcftools Runs Of Homozygosity Option
... The option in VCFtools just outputs all regions where the probability of autozygosity is about 0.99. It is left to the user to filter these events as required.  I've actually made a few changes to the LROH option in the past couple of days, so the function should be a little more informative (and r ...
written 2.6 years ago by Adam940
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Answer: A: Good value of r2 in pruned data
... For PCA, the well-known Novembre 2008 paper used the following:  "First, before running PCA we used the PLINK software to exclude SNPs with pairwise genotypic r2 greater than 80% within sliding windows of 50 SNPs (with a 5-SNP increment between windows)" http://www.ncbi.nlm.nih.gov/pmc/articles/PM ...
written 2.7 years ago by Adam940
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Answer: A: Picking random SNPs from 1000 Genomes using Vcftools
... There's no simple way of doing this directly in vcftools (although using 'sample' seems a good suggestion). However, perhaps you could use the --thin command to achieve what you need? ...
written 2.7 years ago by Adam940
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Answer: A: HaploView error messages for HapMap3 and 1000Genomes phase 3 data!
... The Phase 3 data includes many multiallelic sites. Such sites aren't supported by haploview, and would therefore need to be removed in order to view in haploview. You could do this using, for example, vcftools with the --max-alleles option. ...
written 2.9 years ago by Adam940
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Comment: C: what is the difference between GRCh37 and hg19 ?
... Although this is basically true, GRCh37 has a number of patches, which won't be included in hg19. ...
written 2.9 years ago by Adam940

Latest awards to Adam

Appreciated 16 months ago, created a post with more than 5 votes. For A: From Blog Posts To Research Papers; Successful Cases?
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Sequence Haplotypes From 1Kg Project Variants
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Filtering Vcf File For Fixed Substitutions
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How Were Snps On The Affy Cytoscan Hd Chosen?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Vcftools
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How To Perform A Fst (Fixation Index) Calculation Over A Vcf File Using A Slidin
Scholar 2.5 years ago, created an answer that has been accepted. For A: 1000G high coverage depth of sequencing?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: From Blog Posts To Research Papers; Successful Cases?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: How To Perform A Fst (Fixation Index) Calculation Over A Vcf File Using A Slidin
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Sequence Haplotypes From 1Kg Project Variants
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: From Blog Posts To Research Papers; Successful Cases?
Good Answer 3.6 years ago, created an answer that was upvoted at least 5 times. For A: Sequence Haplotypes From 1Kg Project Variants
Voter 3.6 years ago, voted more than 100 times.
Supporter 3.6 years ago, voted at least 25 times.
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: How To Perform A Fst (Fixation Index) Calculation Over A Vcf File Using A Slidin
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: What Are Numbers Every Bioinformatician Should Know?
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Sequence Haplotypes From 1Kg Project Variants
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Filtering Vcf File For Fixed Substitutions
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: From Blog Posts To Research Papers; Successful Cases?
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Using Tabix And Vcf Tools To Get Cnv / Sv Frequencies From 1000 Genomes Data
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Changing Genome Coordinates For Vcf
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Concordance Of Ngs Data To Wg Snp Array Data

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