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!