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RUFUS k-mer based genomic variant detection
This project forked from marthlab/rufus
RUFUS k-mer based genomic variant detection
Steps to reproduce variants not called by RUFUS that are in the gold-standard data set:
(Notes from S. Gardiner)
Files to reproduce:
So, I've been looking at the RUFUS run from the merged bams of EA/NC/LL with this file path:
/scratch/ucgd/lustre-work/marth/u0880188/smaht/hcc1395_seqc2/merged_runs/EA_NC_LL
How to identify variants that do have contigs made, but don't have calls in vcf:
But, the way I did it previously was I ran bedtools coverage on this file that contains contigs:
/scratch/ucgd/lustre-work/marth/u0880188/smaht/hcc1395_seqc2/merged_runs/EA_NC_LL/EA_NC_LL_3_merged_tumor.bam.generator.V2.overlap.hashcount.fastq.bam
at the specific sites from the validated vcf that RUFUS failed to call.
This gave me this file: /scratch/ucgd/lustre-work/marth/u0880188/smaht/hcc1395_seqc2/merged_runs/EA_NC_LL/contig_depth.txt
Where i then just used a python script to pull out locations that had at least a coverage of 1.
Here is a tsv file of that:
/scratch/ucgd/lustre-work/marth/u0880188/smaht/hcc1395_seqc2/merged_runs/EA_NC_LL/contig_variants_validated.tsv
Looks like there were 1209 variants
Where are the genentech ones?
Re-read the paper to see if any other two letter codes that we need to incorporate in our analyses?
Where are the low and medium quality vcf files?
Evaluate existing performance of RUFUS:
Option A
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