VarScan

[nguyendofx]

Hello All,


Does anyone use Varscan for variant calling?
I use VarScan for calling SNPs. Here is example run command:

#VarScan.v2.3.2.jar mpileup2snp Sample_7.mpileup --variants --min-coverage 1 --min-avg-qual 10

Summary Reuslt:

Chrom Position Ref Var Cons:Cov:Reads1:Reads2:Freq:P-value StrandFilter:R1+:R1-:R2+:R2-val SamplesRef SamplesHet SamplesHom SamplesNC Cons:Cov:Reads1:Reads2:Freq:P-value
chr1 6950751 T C Y:26:20:6:23.08%:1.1309E-2 Pass:9:11:3:3:1E0 0 1 0 0 Y:26:20:6:23.08%:1.1309E-2
chr1 16948372 G A R:10:8:2:20%:2.3684E-1 Pass:5:3:1:1:1E0 0 1 0 0 R:10:8:2:20%:2.3684E-1

...

215347 bases in pileup file
507 variant positions (158 SNP, 349 indel)
78 were failed by the strand-filter
230 variant positions reported (158 SNP, 72 indel)

My question is why there are 72 indels. It should be all SNPs.

Thanks,
Ng

[dkoboldt]

Ng, I think that happened because you used the "--variants" flag, which overrides your command (mpileup2snp) and outputs both SNPs and indels. Remove that flag and you should be good to go.