User: melania 2282

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melania 228290
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Posts by melania 2282

<prev • 81 results • page 1 of 9 • next >
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Simons Diversity Project
... Hello I downloaded phased data from this link [SGDP phased data][1] [1]: https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/phased_data/ 1. Could you confirm that hg38 assembly was used for this data set ? 2. What is the difference between PS2 and PS3 ? Thank you very much ...
genome assembly alignment written 4 days ago by melania 228290
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Comment: C: Refrence datasets for imputation
... yes both of them grch 38 ...
written 20 days ago by melania 228290
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Refrence datasets for imputation
... Hello ! I would like to use two different datasets for genotype imoputation : 1/ 1000G data 2/ Simons foundation project data I tried to combine both data sets but there are many different reference allels between both data sets. Could you suggest any easy way to combine them ? If not, I am us ...
imputation snp written 20 days ago by melania 228290
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Comment: C: CrossMaps tool failure mapping
... Thank you ATpoint, but i think such tool could update the positions accordind to the new assembly ? ...
written 24 days ago by melania 228290
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CrossMaps tool failure mapping
... Hello, I tried CrossMaps tool to update genotyping data from Grch37 to grch38. But I noticed that for each chromosome at least 30% failed to map, this rate of failutre is it acceptable ? Thank you very much ...
grch37 grch38 snp written 24 days ago by melania 228290
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Comment: C: Imputation results from TOPMED server
... When I tried to annotate with VEP tool ( ensembl) it add 1 automatically for each position, so i thought it could be an imputation error .... ...
written 6 weeks ago by melania 228290
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Comment: C: Imputation results from TOPMED server
... Hi Nicolas, For example the first line the variant is chr1:1090809**33**:A:G and the position is 1:1090809**34**-1090809**34**. The VCF file : CHROM POS ID REF ALT QUAL FILTER INFO FORMAT chr22 10522162 chr22:10522162:G:A G A . PASS ...
written 6 weeks ago by melania 228290
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Imputation results from TOPMED server
... Hello, I used the TOPMED imputation server to impute my data, originally Grch37. As explained the server update the data to Grch38 and impute The results are without any RS ID , the names are the position -1 (below), is this accespted result or there is an error ? Thank you very much for your ...
imputation snp topmed written 6 weeks ago by melania 228290
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Comment: C: Imputation output from TOPMED server
... Thank you very much curious :) ...
written 9 weeks ago by melania 228290
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Imputation output from TOPMED server
... Hello, As beginner and it's my first imputation, I have few questions about TOPMED imputation server please any one used to this type of imputation server could help : ) 1. The output of the imputation does it contain typed and untyped SNPs ? 2. If yes how to know the typed ones ? 3. When a f ...
imputation snp topmed written 11 weeks ago by melania 228290 • updated 11 weeks ago by zx87549.6k

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Supporter 9 months ago, voted at least 25 times.

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