Converting vcf to fasta format
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9.1 years ago
JW ▴ 10

Hello,

I have a set of vcf files created by aligning reads to a reference and then creating a smalls pileup. Now, I would like to create a fasta file for each vcf file but instead of using the ambiguity codes I would like to take the major variant in the case of multiple options. Which software could I use to do that?

Thanks in advance

PS.: If somebody knows where the information about variant abundance in vcf is, please tell me as I could then write a script solving the problem described above.

fasta samtools vcf alignment next-gen • 7.6k views
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as pointed out before, this is a recurrent question. for instance, you may find it already addressed in Introducing Known Mutations (From A Vcf) Into A Fasta File. please use the search box before asking.

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See this relevant post Modifying fasta file based on vcf information , although I don't think the problem was fully resolved. It would be good to paste a few lines from your vcf file along with some meta information.

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