Which Parameters Are You Using For Samtools Mpileup And Bcftools To Compare Human Cells To See Individual Differences?

Question

[Deniz]

Which parameters are you using for samtools mpileup and bcftools to compare human cells to see individual 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? I really appreciate any help!

thanks

[Lars Juhl Jensen]

I edited your question to make sentences start with capital letters and not have almost every sentence end with multiple question marks.