User: freeseek

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freeseek30
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Posts by freeseek

<prev • 7 results • page 1 of 1 • next >
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Answer: A: How To Convert Illumina/Affy Array Data To Vcf Format
... I wrote affy2vcf, a bcftools plugin that is capable of generating VCF files out of the output of the Affymetrix apt-probeset-genotype command line tool. ...
written 10 weeks ago by freeseek30
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Answer: A: Illumina BeadArray GTC to VCF conversion
... I wrote gtc2vcf, a high performing bcftools plugin to convert Illumina GTC files to VCF on Linux. It can also be made to work with IDAT files. Some features are currently missing (as of 2018-07-11) but I plan to include them in the future if there is demand. ...
written 4 months ago by freeseek30
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Answer: A: How to extract raw genotype calls from idat or gtc illumina files
... I wrote gtc2vcf, a high performing bcftools plugin to convert Illumina GTC files to VCF on Linux. It can also be made to work with IDAT files. Some features are currently missing (as of 2018-07-11) but I plan to include them in the future if there is demand. ...
written 4 months ago by freeseek30
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Answer: A: How to Convert Illumina reports to Vcf files?
... I wrote gtc2vcf, a high performing bcftools plugin to convert Illumina GTC files to VCF on Linux. It can also be made to work with IDAT files. Some features are currently missing (as of 2018-07-11) but I plan to include them in the future if there is demand. ...
written 4 months ago by freeseek30
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Answer: A: Read binary Illumina GTC files (1000 genomes)
... I wrote gtc2vcf, a high performing bcftools plugin to convert Illumina GTC files to VCF on Linux. It can also be made to work with IDAT files. Some features are currently missing (as of 2018-07-11) but I plan to include them in the future if there is demand. ...
written 4 months ago by freeseek30
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Answer: A: Illumina HumanOmniExpress IDAT files
... I wrote gtc2vcf, a high performing bcftools plugin to convert Illumina GTC files to VCF on Linux. It can also be made to work with IDAT files. Some features are currently missing (as of 2018-07-11) but I plan to include them in the future if there is demand. ...
written 4 months ago by freeseek30
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Answer: A: How To Grep A Specific Contig From A List?
... If you want to extract multiple contigs at different times, it is highly suggested that you build an index. Here some commands: samtools faidx in.fasta (create an index for the fasta file with all the contigs) samtools faidx in.fasta contigname > contigname.fasta (extract the single contig you ...
written 6.3 years ago by freeseek30

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