replacing specific positions in fasta from vcf/list

[kpboh]

I have a reference assembly (in fasta format) and vcf file containing a list of specific sites. I'd like to edit the fasta file to change these positions to 'Ns'.

Does anyone have any suggestions for a tool to accomplish this? I also have a trimmed down version of the vcf that just contains chrom# and position...

Thanks in advance for any suggestions!

[neavemj]

Sounds like a job for python or perl.

You could read through the vcf file and gather the positions in a dictionary. Then read through the fasta file and make the change to N at positions that match in the dictionary..

[kpboh]

thanks for the reply. yeah--seems to be the way to go, but i'm unfortunately not fluent enough in either language.

i did find this example but couldn't get it to run properly (it output an entire new fasta for each individual position as it looped through the vcf instead of accumulating all the changes in the vcf before printing a single, mutated fasta). i suspect it's a trivial change to get it to work properly.

at any rate, i managed to hack a solution by changing the 'alt' allele in my vcf to 'N', modifying (using sed) all the GT values to "1/1", then feeding this file into GATK's FastaAlternateReferenceMaker tool. clearly far from elegant, but i checked the positions in question in the output and it seemed to have worked.

[neavemj]

Clever solution!