Generating fasta from VCF with only the variant
Hi Stars,
I did an alignment and from that, I called the variant (VCF). So my question is how I can convert that vcf into fasta with the only predicted variant, not consensus. I know usually for consensus we will do it with GATK Fasta Alternate Reference or BCF tools.
Excepted fasta out as like this (If there is no variation, that position must be noted with N)
>Seq1
NNNNNANNNNTNNNNNNGNNNNNNNNNC
Any ideas?
• 1,384 views
•
link
written
by
the_cowa •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
VCF to fasta incorporating heterozygous sites
written by Sarah •
-
Building vcf from most common alleles
written by Eugene •
-
Annotating variants from a sequence and list of position-specific variants
written by manaswwm
-
Generating Positional List from VCF
written by Ared445 •
-
Problems with overlapping variants in a vcf file
written by Buxus •
-
VCF to Fasta with out reference
written by the_cowa •
-
Consensus VCF file from several variant callers
written by ajuiwl •
-
samtools mpileup output only contains vcf header
written by s102060125 •
-
Alignment & Variant Calling explanation SNP and SNV.
written by ernestrv0101 •
-
vcf-consensus outputs sequence same as reference
written by seretnacho •
What is the purpose of this exercise?
I am trying to generate a new gene sequence from an known reference, so I am not interested the same reference sequence
You should be able to write some code to fetch reference sequences and apply any variants, as long as they are in HGVS nomenclature. Read the python hgvs package documentation for a basic understanding of how you can interact with posedit components.