User: andrewl

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andrewl10
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Posts by andrewl

<prev • 12 results • page 1 of 2 • next >
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Meaning of 'tag' in the context of variants
... I would like to understand what the meaning of 'tag is in the following paragraph. Does it mean "correlated with" or does it somehow act on the tagged gene? > The supplementary meta-analyses confirmed one additional independent locus that showed genome-wide significant association with CM (rs741 ...
interpretation variant written 9 weeks ago by andrewl10 • updated 24 days ago by Dan Gaston6.8k
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Calculating ethnicity of a sample VCF
... I'm looking to understand how best to calculate estimated ethnicity from a sample VCF. That is to take a VCF file and estimate that the person that the file came from is 80% caucasian and 20% asian. At least to the level of the 5 super-populations of the 1000 genomes project, and even better if to t ...
ancestry written 9 weeks ago by andrewl10 • updated 9 weeks ago by GabrielMontenegro330
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Weird translated refs between hg19 and hg38
... I'm possibly doing something wrong but having problems converting from hg19 to hg38, where my reference call is changed (which changes the user call). I tracked down one example that is reproducible: `#CHROM POS RSID REF ALT QUAL ALLELES` `8 129076572 rs13255292 ...
vcf crossmap hg38 written 3 months ago by andrewl10
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Understanding typical GWAS versus clinvar studies
... I'm new to genomics and I'm trying to get my head around the findings of typical pathogenic studies reported in clinvar and those reported in other snp databases such as GWAS. And how to relate them. I'm interested in understanding the general case - I imagine there are exception in both. **Clinvar ...
gwas clinvar written 3 months ago by andrewl10
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Comment: C: Broad rules of thumb on # of variations
... I'm looking for something that doesn't require actually looking at the variants. Of the few WGS VCFs I have see, they tend to have 4-5M rows, so I would have though the WES which read ~1% of the genome would have on average around 40-50K variations. Can I not just count rows and draw a conclusion ba ...
written 3 months ago by andrewl10
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5 follow
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Broad rules of thumb on # of variations
... I'm looking for some broad rules of thumb for how many variations to expect for WGS versus WES. The idea being that if I am given a VCF of unknown origin and coverage, what does the number of rows in the VCF help tell me about whether it was derived from an WES or WGS sequence. Or are there any ot ...
variations dna written 3 months ago by andrewl10 • updated 3 months ago by H.Hasani580
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Comment: C: Reality check: insertion v duplication
... Wow - thanks I was expecting that this was a silly question to answer, now glad I did. ...
written 4 months ago by andrewl10
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Reality check: insertion v duplication
... Quick reality check - I have been normalizing VCFs and annotation files according to this methodology: Tan A, Abecasis GR, Kang HM. Unified representation of genetic variants. An example implementation would be this here: https://github.com/ericminikel/minimal_representation/blob/master/normal ...
normalization dna written 4 months ago by andrewl10 • updated 4 months ago by harold.smith.tarheel3.8k
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Normalizing fails due to incorrect column count
... I have a reasonably standard VCF file: `##source=freeBayes v0.9.15-3-g6022d6a` `##reference=/vbin/ref/hg19.fa` ` ...` `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown Sample1` `chr10 61372 . CAT CT 285.58 PASS AB=0;ABP=0;AC=4;ADP=10;AF=1;A ...
vcf normalize written 4 months ago by andrewl10
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Comment: C: Identify recessive conditions from VCF files
... Thanks - this is great. I only have access to the VCF, so as I would understand from your answer, it is not possible from that file alone to perform any analysis to determine phase. Correct? I guess I was curious if there was anything in the metadata of a VCF file that helped for this .... ...
written 5 months ago by andrewl10

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