Is there any way to write my mutation dataframe to vcf file?
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vinod.acear ▴ 50
@vinodacear-8884
Last seen 3.6 years ago
India

I want to save a mutation data avalable in df format to a .vcf file, But not getting any way to do this. Please advise

> head(sample.mut.ref)
  Sample  chr      pos ref alt
1      1 chr1   905907   A   T
2      1 chr1  1192480   C   A
3      1 chr1  1854885   G   C
4      1 chr1  9713992   G   A
5      1 chr1 12908093   C   A
6      1 chr1 17257855   C   T
> typeof(sample.mut.ref)
[1] "list"
> class(sample.mut.ref)
[1] "data.frame"

writevcf vcfr mutationalpattern deconstructSigs synbreed • 2.1k views
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shepherl 3.8k
@lshep
Last seen 12 hours ago
United States

Unfortunately there is no easy way to do this. Your best bet is to look at the vcf constructors in VariantAnnotation package. You could coerace your data.frame into a vcf object using the constructors and then use the write.vcf function.

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