mpileup and pileup results

[rururara]

Hi everyone.

1. I tried to call the snps using both mpileup and pileup.
There is more differences in snps calling numbers.
I found that mpileup give me less snps compared too pileup which produce lots of snps calling.
eg pileup = about 10 K snps while mpileup = about 800 snps

i run using this command
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf

is using mpileup is more thorough compared to pileup?

btw, i call the snps from rice data.

2. can anyone here explain how can i make use the genotype data that present in vcf 'FORMAT' ? I read already in the documentation but not really understand.

Thanks all!

[colindaven]

According to the documentation from Samtools pileup is now depreciated. Use mpileup.

Apparently the algorithm is more complex, takes into account local realignment of reads around putative SNP positions and also can modify base qualities around these positions. See the part on BAQ in the mpileup docs.
Probably mpileup is reducing the number of false positives here, but have a look at some of the data. I'm sure you'll see some patterns emerging.