Question: How to make new VCF files myself?
0
gravatar for Amirosein
2.7 years ago by
Amirosein70
UBC, Vancouver, CA.
Amirosein70 wrote:

Hi

I'm doing some computations on sanger seq. data.

for example i have a read, i aligned it to the reference genome and found an SNP, now i want to make a new VCF file for using in other tools like Annovar or SIFT, how to do this? (specially in Rstudio/Bioconductor)

"VcfR" is not published yet and i could not find any related function in "VariantAnnotation" package

Edit: finally i decide to write a function myself, it seems not hard, but first is there anybody wrote a function before?

thanks all

variantannotation variant vcf • 1.0k views
ADD COMMENTlink modified 2.6 years ago by chen1.8k • written 2.7 years ago by Amirosein70
1

It should not be difficult to make a VCF from scratch unless you want to make a multisample VCF. Can be done with simple Awk. What information do you have and how the file looks like ?

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by geek_y9.4k
1
gravatar for chen
2.6 years ago by
chen1.8k
OpenGene
chen1.8k wrote:

Take a look at VCF spec doc, https://samtools.github.io/hts-specs/VCFv4.2.pdf

Follow the spec, write the file directly by yourself. It is not difficult.

ADD COMMENTlink written 2.6 years ago by chen1.8k
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