Question: A weird variant call from VarScan2 mpileup2snp
gravatar for rayliu0115
2.2 years ago by
rayliu01150 wrote:

Hi there,

I used VarScan.v2.4.3.jar mpileup2snp to call mutations with -min-coverage=100 and --min-var-freq= 0.01 and I got some weird variants. For example, one mutation for the output is :

21 42848562 . G C . PASS ADP=866;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:866:866:6:5:45.45%:9.8E-1:36:34:4:2:3:2

Usually, DP=RD+AD=RDF+RDR+ADF+ADR and FREQ=AD/DP=(ADF+ADR)/(RDF+RDF+ADF+ADR), but in this case RD+AD=11, not equal to DP=866. Frequency should be 5/866=0.6%, also not equal to 45.45%.

How to explain this variant? Which value should I choose to filter? Does anyone have any idea?

Thanks so much! Rui

ADD COMMENTlink written 2.2 years ago by rayliu01150

My first option would be to visually inspect the BAM with IGV or similar and see if I can make sense of the numbers.

ADD REPLYlink written 2.2 years ago by bernatgel2.6k
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