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Old 05-23-2013, 04:03 PM   #1
kasthuri
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Default Extracting REF and ALT from VCF

This may be a simple question.

I am trying to extract CHR, POS, REF and ALT and other info from a VCF file to a txt file using vcftools. Can somebody point me how to get REF and ALT? I don't get this information but everything else.

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-K.
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Old 05-23-2013, 04:36 PM   #2
id0
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I think vcf-to-tab does exactly that:
vcf-to-tab < file.vcf
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Old 05-23-2013, 04:51 PM   #3
kasthuri
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Quote:
Originally Posted by id0 View Post
I think vcf-to-tab does exactly that:
vcf-to-tab < file.vcf
Thank you, id0. It works and I get the genotypes. But I don't get other information from the FORMAT fields. I know I can use --extract-FORMAT-info separately and 'paste' these two lists, but I would be more comfortable if I can get the genotypes as well as the format fields information at the same time. Anyway, I thank you for the solution.
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Old 05-23-2013, 04:55 PM   #4
kasthuri
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Quote:
Originally Posted by kasthuri View Post
Thank you, id0. It works and I get the genotypes. But I don't get other information from the FORMAT fields. I know I can use --extract-FORMAT-info separately and 'paste' these two lists, but I would be more comfortable if I can get the genotypes as well as the format fields information at the same time. Anyway, I thank you for the solution.
Also, I will be just happy with the ALT entries instead of actual variants. Is it possible to get that?

Thanks
-K.
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Old 05-23-2013, 09:16 PM   #5
swbarnes2
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vcf's are naturally text files. If yours isn't, it's just compressed, so uncompress it.
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Old 05-24-2013, 07:00 AM   #6
kasthuri
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Quote:
Originally Posted by swbarnes2 View Post
vcf's are naturally text files. If yours isn't, it's just compressed, so uncompress it.
Thank you swbarnes2. I found VariantsToTable in GATK does exactly what I wanted.
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