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4.7 years ago
gab ▴ 20
I got circa 130 high confidence somatic SNP, comparing tumor and blood samples with VarScan. I wanted to annotate them so I passed the data to VarAft, but it gives me just 6 variations. What am I doing wrong? Is there a tool that gives me the info i can get with VarAft?
Have you thought in annotating this file with other tool than VarAft. If it works for all your variants, the problem is with VarAft. It it works for your 6 variants only, the problem is in your input file.
It may be helpful to give us a sample of your somatic variants here.
This is some example of .snp output from VarScan. Annotating with VEP gives no problems.
Are these coordinates on GRCh37 or GRCh38? If the VEP runs fine with your input file, the chances are there is something going on with VarScan.
Can you compare the 6 positions that work with VarScan with the ones that do not work? What is different between this two groups?
It turned out bam files were generated with a different fasta instead of the one I used to get the mpileups, this lead to indexing problems and all SNPs were misplaced. Tahnks to everybody for the help!
Does the tool remove variants that are unlikely to be related to disease? If so, I would not be surprised that the majority of mutations got eliminated. Most somatic mutations have no causality towards the disease but are passengers.