Documentation for output files

[kartikchandran]

Hi there,

I was wondering if you could help me find the documentation for the fields in the SNVS_final.csv file and the cooccuring_mutations.csv file. I've uploaded the files generated from my VILOCA run.

Many thanks,
Kartik

SNVs_0.010000_final.csv
cooccurring_mutations.csv

[LaraFuhrmann]

Hi Kartik,

the description of the columns in SNVs_0.010000_final.csv is in the header of SNVs_0.010000_final.vcf:

##INFO=<ID=Fvar,Number=1,Type=Integer,Description="Number of forward reads with variant">
##INFO=<ID=Rvar,Number=1,Type=Integer,Description="Number of reverse reads with variant">
##INFO=<ID=Ftot,Number=1,Type=Integer,Description="Total number of forward reads">
##INFO=<ID=Rtot,Number=1,Type=Integer,Description="Total number of reverse reads">
##INFO=<ID=Pval,Number=1,Type=Float,Description="P-value for strand bias">
##INFO=<ID=Qval,Number=1,Type=Float,Description="Q-value for strand bias">
##INFO=<ID=FreqX,Number=1,Type=Float,Description="Frequency of the variant in window X">
##INFO=<ID=PostX,Number=1,Type=Float,Description="Posterior probability of the variant in window x">

Since each position is covered by three windows (=local regions) you have three colums for Freq and Post.

The file cooccurring_mutations.csv contains one row per occurrence of a mutation in each haplotype, listing all haplotypes where a mutation is present. Note that the posterior threshold is not applied here. The columns are as follows:

haplotype_id: Name of the haplotype sequence as in the fasta files in `haplotypes/`
chrom: Name of reference sequence 
start: Start position along the genome of local haplotype 
reads: Number of reads that were assigned to haplotype
support: Posterior probability of the haplotype. 
coverage: Total number of reads considered in local region 
position: Genome position of variant
ref: Reference base at position
var: Variant base at position

I hope that makes things clear.