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Posts by rayliu0115
... 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 ...
... Dear all, I have a question about the different results for one same tumor sample between VarScan2 somatic and mpileup2snp. I used VarScan2 somatic to find somatic variants and germline variants from one pair of tumor-normal matched samples with the code below: samtools mpileup -d 1000000 -q 30 - ...
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