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
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
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