Data reformat (.vcf file)

usegalaxy.org support
#1

I’m curious if anyone could help me to reformat a file that only has sequencing positions to a standard .vcf file. The file format I have is:
#CHROM POS
I 1006
I 2527
I 5391
…
And I need to transform them into this format:
##fileformat=VCFv4.1
##samtoolsVersion=0.1.18 (r982:295)
#CHROM POS ID REF ALT QUAL FILTER INFO
chrI 1222 haw1 A C . . MPU=-21.9682
chrI 2651 haw2 T A . . MPU=-21.9337
chrI 3659 haw3 C T . . MPU=-21.9094
…

I appreciate any help and suggestion. Many thanks!
-TY

#2

Hi,
There are some tabular- and text-dealing tools at Galaxy.
Can you point out where did your first file come and what tool you are planning to use with the second one?

#3

The REF and the ALT allele are required fields in VCF so if you really do not have that information there isn’t much you can do.

#4

Thank you for the reply @David and @wm75. The first file comes from a customized SNP analysis package. The author used various variants calling tools on two files and only extract the position information. I guess the solution is to re-do the variants calling to get the complete vcf files, then cross-reference the list to those files.

#5

Maybe you can contact the author to provide the complete files. Or check if they have any supplemental files containing it.