A weird variant call from VarScan2 mpileup2snp

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5.9 years ago

rayliu0115 • 0

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

VarScan2 mpileup2snp variant calling • 1.4k views

ADD COMMENT • link 5.9 years ago by rayliu0115 • 0

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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 REPLY • link 5.9 years ago by bernatgel ★ 3.4k

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