User: Wan Shi Tong

gravatar for Wan Shi Tong
Wan Shi Tong60
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Posts by Wan Shi Tong

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Comment: C: Imputation of vcf file
... plink --vcf file.vcf --recode A --out file_matrix ...
written 4 months ago by Wan Shi Tong60
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Comment: C: Merge VCFs with overlapping samples
... Yeah, that is exactly my problem. vcf-merge and bcftools merge do not merge same samples. They create new entries for each repeated sample unfortunately. ...
written 10 months ago by Wan Shi Tong60
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Merge VCFs with overlapping samples
... I have VCFs that have some overlapping samples, is there a tool that can do this... ###VCF1: CHR POS ID ALT REF QUAL INFO FILTER FORMAT Sample1 Sample2 Sample3 SNP1... SNP2... SNP3... --- ###VCF2: CHR POS ID ALT REF QUAL INFO FILTER FORMAT Sample2 Sample3 Sampl ...
vcf tools snp written 10 months ago by Wan Shi Tong60 • updated 9 months ago by omg what am I doing60
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Answer: A: Need sample vcf file containing Complete Exome sequences
... Try VCFs from the 1000 Genomes Project. Or VCFs in the NCBI. ...
written 11 months ago by Wan Shi Tong60
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Answer: A: How to get imputation accuracy/quality after using IMPUTE2?
... I actually figured it out. Incase anyone ever has the same question. IMPUTE2 outputs a file called info where it has imputation quality information. Depending on the command line arguments you choose you can get more specific statistics. https://mathgen.stats.ox.ac.uk/impute/output_file_options.html ...
written 11 months ago by Wan Shi Tong60
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How to get imputation accuracy/quality after using IMPUTE2?
... I know I might be missing something obvious, but how do I get the accuracy/quality of my imputation after using IMPUTE2 (or any imputation tool)? How is the quality of an imputation measured? Thank you! ...
impute2 impute statistics written 11 months ago by Wan Shi Tong60

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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to get imputation accuracy/quality after using IMPUTE2?

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