Failed to convert vcf (an output from Lumpy) to var format (input of SVEngine)

[Former user]

Hi SVEnginer,

I would like to generate fasta file from lumpy output vcf and hg19 by using SVEngine. The first step is converting the vcf to var format. I noticed that there is a script called vcf2var.R in SVEngine. So I used it for this purpose. I have several questions concerning vcf2var.R: 1. lumpy vcf is the right format for it? It keeping saying the vcf missing some fields. 2. What does the repbase.rm.fasta content? Where I find it for human hg19 or hg38? Thank you for your help. Loi

[Charlie Xia]

Hi Loi,

vcf2var.R is provided as is (which i am not interring to maintain as changes by tools to their output format could vary by time). And you don’t have to use it to convert bed-like files to var format for input to SVEngine, for example use bedpost or bedtools.

1. if you haven’t fixed, would like provide your input that i can run and reproduce your error.
2. repbase.rm.fasta is a git-lfs file, you shall use git-lfs to pull it down and view content. see https://git-lfs.github.com

Sorry for my awful slow response.

Charlie

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