What is read depth -D100 means in samtools?

[ketan_bnf]

Hi all,

I am working with exome reads, i extracted SNP and indels using,

# samtools mpileup -ugf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
# bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf

i don't know what -D read depth means in vcfutils.pl?

i am having 101245 reads FYI.

[Shambala]

The -D option of varFilter controls the maximum read depth, which should be adjusted to about twice the average read depth.