annovar mpileup2cns and mpileup2indel give different results

Question

[Assa Yeroslaviz]

Is anyone still using annovar nowadays? Is there a better tool for variant detection out there?

I was wondering why I get different number of indes when running the two commands -mpileup2cns and mpileup2indel with the same statistical parameters (thresholds).

when looking only for indels:

java -jar ~/software/varscan/VarScan.v2.4.4.jar mpileup2indel mpileup/1.mpileup --output-vcf 1  --mincoverage 10 --min-var-freq 0.10 --p-value 0.1 > VarCalling/1.varScan.indel.vcf
Only indels will be reported
Min coverage:   8
Min reads2:     2
Min var freq:   0.1
Min avg qual:   15
P-value thresh: 0.1
Reading input from mpileup/1.mpileup
873085870 bases in pileup file
516984 variant positions (511729 SNP, 5255 indel)
97612 were failed by the strand-filter
5030 variant positions reported (0 SNP, 5030 indel)

but when looking for both:

$ java -jar ~/software/varscan/VarScan.v2.4.4.jar mpileup2cns mpileup/1.mpileup --output-vcf 1  --mincoverage 10 --output-vcf 1 --min-var-freq 0.10 --p-value 0.1 > VarCalling/1.varScan.cns.vcf
Min coverage:   8
Min reads2:     2
Min var freq:   0.1
Min avg qual:   15
P-value thresh: 0.1
Reading input from mpileup/1.mpileup
873085870 bases in pileup file
516984 variant positions (511729 SNP, 5255 indel)
97612 were failed by the strand-filter
516984 variant positions reported (511729 SNP, 5255 indel)

Why do I find with the consensus search more indels?

thanks Assa