Entering edit mode
5.3 years ago
Myo Naung
▴
10
Hi,
Do anyone know how to convert VCF files into FASTA files such as using R ?
Myo
Hi,
Do anyone know how to convert VCF files into FASTA files such as using R ?
Myo
Please do not use convert
when dealing with data formats with non-equivalent information content. You cannot convert
VCF to FASTA, you can combine alternate allele information from a VCF into a reference FASTA to get FASTA that incorporates a specific percentage of the ALT alleles into itself.
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Hello Myo Naung ,
what do you expect by this "conversion"? A
vcf
file contains information about differences compared to a given reference. What you can do is: Take your reference sequence and integrate your variants. This is called a consensus sequence. bcftools consensus is one tool that can do this (if this is what you want to do).fin swimmer
Hello fin swimmer,
Thanks for the suggestions. What I would like to do is to calculate neutrality statistics like Tajima's D, and there I would like to see TD values of variant sites related to conserved regions. Not sure I can do directly from vcf.
Myo
Hi fin swimmer, creating consensus reference genome for a specific human population can be considered as a alternative for de novo genome assembly?