User: Vivek
Vivek • 1.9k
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Posts by Vivek
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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 5 weeks ago by
Vivek • 1.9k
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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 6 weeks ago by
Vivek • 1.9k
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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 6 weeks ago by
Vivek • 1.9k
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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 7 weeks ago by
Vivek • 1.9k
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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 7 weeks ago by
Vivek • 1.9k
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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 8 weeks ago by
Vivek • 1.9k
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... 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
Vivek • 1.9k
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... 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
Vivek • 1.9k
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... 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
Vivek • 1.9k
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... 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
Vivek • 1.9k
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