User: NS

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NS0
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Posts by NS

<prev • 7 results • page 1 of 1 • next >
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Comment: A: Read binary Illumina GTC files (1000 genomes)
... How do you create a manifest file required for Illumina's GTCtoVCF python source. I have the idat and gtc file but not the manifest file. Can someone please tell me how can I generate that ? Thanks ...
written 3 months ago by NS0
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How to create manifest file for Illumnina GTCtoVCF
... Hi I have several idat and gtc files. I want to convert them to standard vcf format to obtain the genotype information. I found that llumnia has developed a python source for parsing gtc files (https://github.com/Illumina/GTCtoVCF). However it requires manifest file / Bead pool manifest. The dat ...
genotype gtc idat illumnia sequencing written 3 months ago by NS0
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Answer: A: genotyping according to the red/green intensity for illumina microarray?
... Hi Were you able to process the idat files and convert them into standardized format such as Plink or VCF ? I am struggling with the same thing and have no idea of how to convert idat/gtc files to plink format ? Please let me know if you found the solution. Thanks ...
written 3 months ago by NS0
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Comment: C: Extracting Ancestral allele from INFO column of vcf file
... Thanks for your help ! Is there also a way to keep only bi-allelic SNPs in this output using bcf tools ? ...
written 5 months ago by NS0
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Extracting Ancestral allele from INFO column of vcf file
... Hi From my vcf file, I need to generate a text file with the following headers (shown just an example): CHROM POS ID REF ALT AA 1 886817 rs11174805 C G C 1 886817 rs111111111 C T . 1 886817 rs11144444 A T ...
vcf ancestral allele snp shell linux written 5 months ago by NS0
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Comment: A: Reference and ALT allele list for all SNPs
... Thanks ...
written 5 months ago by NS0
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Reference and ALT allele list for all SNPs
... Where can I find the list of REFERENCE and ALT alleles for all SNPs (hg19/GrCH37)? Can someone please share a link where I can download the list. Thanks ...
snp written 6 months ago by NS0

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