I have some questions regarding the readouts of VarScan.
I ran VarScan (SNP and Indel) on my BAM pileup, and imported the vcf data to igv.
1st question: I got 2 tracks for each imported vcf on igv. The upper track presents gray bars as detected variants; the lower track (automatically named sample 1) presents blue (or light blue) bars. I do not understand why it is presented in this way, and what the different colors indicate.
2nd question: When I move my cursor to the bars, I can see many information regarding this variant call. What does it mean when my “Genotype quality=0” or “QUAL: -10”? My depth for most of the called variants are above 1000, and the “Minimum base quality at a position to count a read” is set as 30 when running VarScan.
3rd question: When I set-up the parameters before execute VarScan, the default value of “p-value threshold for calling variants” is 0.99. I thought it would be more logical to have it as 0.05, so I guess I do not understand what this parameter is asking for. Can anyone explain it to me?
My sincere appreciation,