Hello bioinformatics people.
I know lots of people have issues with VCF files and want to turn them into nice tables using R. I have made a script which does that... sort of.
I can take any sample column in VCF and turn it into a beautiful table, with each colon-delimited statistic in its own cell, but I have not figured out how to automate the process over many samples.
I have already asked this question in details on Stacks Overflow:
http://stackoverflow.com/questions/29604604/r-splitting-up-a-delimited-vcf-file-using-a-for-loop-iterating-over-sev
But thought I would post here to see if anyone else in the biological community had overcame it.
Attached: some example data if you want to play with it.
Hi Joshua, wrote this, see if it helps... It'll generate output as shown in appended shell-dump...
#!/usr/bin/perl -w
use strict;
my $inFile = $ARGV[0];
my @output = ();
open(IN,'
Sounds like a parsing challenge... Do you have any perl/python/similar scripting skills? Parsing flat files isn't something i'd recommend doing in R...
Hey Leon!
I have some knowledge of Python and Unix language. I actually tried this in Python but, had issues because it takes each row as a single list (and each cell within that row contains multiple values separated by ":"), which lead to me being confused as to how to pull strings out of lists within lists.
At the moment R has been the most successful for me; however, I do agree that Python could make life a lot easier - my knowledge of the language is still in development though.
If you have any advice, would be love to hear it.
In the case of multiple samples, are they in a single VCF file or multiple files? Do the samples have different number of statistical measurements (therefore different # of columns after parsing) or do the all have the same number. From your example, it is hard to tell in what scenario/instance you are running into trouble.
Hi Joshua, wrote this, see if it helps... It'll generate output as shown in appended shell-dump...
#!/usr/bin/perl -w
use strict;
my $inFile = $ARGV[0];
my @output = ();
open(IN,'
@Leon: legend!
@Daniel: they are in a single .vcf like that attached.
Hi,
there are programs that can help you like vcftools. You can use this to break down vcf files including multiple samples to one table.
In addition python has a library to handle vcf files (PyVCF). I assume that biopython/ bioperl have also some packages.
R isn't the most convenient for parsing, but if you want to keep your workflow entirely in R, try the following script:
data
We can resolve this issue using vcfR package in R. It reads directly a VCF file (standard) and parse all the parameters to dataframe. Try below script:
vcf=read.vcfR(inFile$datapath,checkFile = TRUE)
my.vcf.df
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology