samtools mpileup and bcftools command lines to compare individual differences?

[aslihan]

Which parameters are you using for samtools mpileup and bcftools to compare individual SNP differences?

Could you write your commands?

I am using:

samtools mpileup -ugf *.fa *.bam *.bam *.bam *.bam
bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | bcftools/vcfutils.pl varFilter -D100 > var.flt.vcf
My question how can I improve my command to get best quality SNPs?

mpileup -ugf ?

What about -6 option or -6 -uDSf? I really appreciate any help!

thanks

[DineshCyanam]

Yes, I am interested in knowing the same... Right now I am using the commands given here: http://samtools.sourceforge.net/mpileup.shtml