In last days I was testing Varscan mpileup and pileup commands. Here are commands that I've used:
1) samtools mpileup -m1 -B -F0.0001 -d5000 -f <reference> <bam> > bam.mpileup
A) VarScan.jar pileup2snp input --strand-filter 0 –min-coverage 3 –min-var-freq 0.1
B) VarScan.jar mpileup2snp input --output-vcf --strand-filter 0 –min-coverage 3 –min-var-freq 0.1
Unfortunately I get different number of SNPs detected. For 1A - 93587 and 1B - 53769. I am comparing results to other tool which predicted variants with the number of 8827. I would like to have results including those 8827 snps. With the use of pileup I have 100% covered but with mpileup only 95,70%.
I need to use mpileup command for VCF output which wll be further use for SNPEff Annotation.
Could anyone help me with this issue?
I would really appreciate for help,