User: Vivek
Vivek • 2.1k
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Posts by Vivek
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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
Vivek • 2.1k
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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
Vivek • 2.1k
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... 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
Vivek • 2.1k
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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
Vivek • 2.1k
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... 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
Vivek • 2.1k
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... 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
Vivek • 2.1k
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... 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
Vivek • 2.1k
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... 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
Vivek • 2.1k
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... 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
Vivek • 2.1k
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... 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
Vivek • 2.1k
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