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zhou-lab / biscuit

BISulfite-seq CUI Toolkit
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Header for snp bed file #26

Open smcnew opened 5 years ago

smcnew commented 5 years ago

Hi: I'm wondering where to find information on what the columns are produced by the vcf2bed -t snp file. I got an output file that has the following columns:

100056 34 35 A G 1/1 G3 3 1.00

I'm guessing the first series is chromosome, start position, stop position, major allele, minor allele, genotype; however I can't figure out what the last three ("G3", "3", "1.00") values refer to. Any help is greatly appreciated.

More generally- if there's an option to add headers to the gc, snp, and other .bed files I'd appreciate knowing how.

Thanks!

zwdzwd commented 5 years ago

Hi I think the last three columns represent the allele support, total read depth, and allele frequency. There is currently not an option to add bed headers. But I will add it to my list.

Best,

smcnew commented 5 years ago

Thanks so much!

Sabrina

On Tue, Dec 18, 2018 at 3:40 PM Wanding Zhou - Bioinformatics < notifications@github.com> wrote:

Hi I think the last three columns represent the allele support, total read depth, and allele frequency. There is currently not an option to add bed headers. But I will add it to my list.

Best,

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