I have used varscan2 and the results below are not clear to me.I compared a tumour to a normal and I am interested in somatic mutation. The following snp is predicted as germline and I expected as somatic but it is not clear to me the reason, Any suggestions? Thanks Marco
##fileformat=VCFv4.1
##source=VarScan2##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: r
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
chr12 49420661 . G A . PASS DP=3204;SS=1;SSC=255;GPV=1E0;SPV=1.5981E-225 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:1843:1835:2:0.11%:1595,240,2,0 0/1:.:1361:828:532:39.12%:740,88,475,57
1 answer
The SNP is found in both your tumor and your normal sample (both have a 0/1 genotype). Therefore it's not somatic but germline.
That's a good point. Although I would expect that if contamination happens it's the other way around. But we don't know how the samples were collected and which type of tumor is studied.
Right, sounds reasonable.
Yes the sounds reasonable, I have to check the settings in varscan. Probably I have to allow to define Germaine above a percentage or number of reads. Any suggestions?
There is the --max-normal-freq flag in ./VarScan2 processSomatic, default is 0.05 so 5% as maximum frequency for normals. Did you reduce that to 1%? If so, try with the defaults. I think this makes biological sense to exactly exclude these kinds of situations you experience right now.
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I think that I will change my setting, since this is in my opinion is a somatic mutation, there only 2 reads in the normal sample (lymphoma). I check how to set varscan option in a way that this should be predicted as somatic. What do you think? Marco
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