Question: how to create a multifasta file from miltisample vcf file?
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gravatar for jcuenca
2.6 years ago by
jcuenca0
jcuenca0 wrote:

Hi everyone. I'd like to create a new fasta file containing all sequences for which I called variants in a vcf file. I can only get one sequence, but I would like to rebuild the sequence for all my samples. I know I can do it individually, but is there any tool to do it for all my samples at once? Thank you very much!

sequencing rna-seq snp alignment • 2.0k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by jcuenca0

How about a simple iteration of vcf-consensus -s <sample_name> . The new version also gives an option to use IUPAC ambiguity codes for hetrozygotes or no-calls.

ADD REPLYlink written 2.6 years ago by microfuge1.0k

See this post. It may be at least partially helpful.

vcf to MAF to fasta

ADD REPLYlink written 2.6 years ago by natasha.sernova3.4k
0
gravatar for jcuenca
2.6 years ago by
jcuenca0
jcuenca0 wrote:

Thank you very much! This is what I actually did, one by one within an iteration. But it is a long pipeline (split the vcf into individual files, bzip, tabix, then vcf-consensus for each one and finally cat all fasta in one file). Also, I end up with many unuseful (intermediate) files (I'm analyzing 48 samples). The vcf to MAF maybe can help.

ADD COMMENTlink written 2.6 years ago by jcuenca0
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