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Old 01-25-2011, 01:12 AM   #1
Location: India

Join Date: Oct 2010
Posts: 59
Default What is read depth -D100 means in samtools?

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 | varFilter -D100 > var.flt.vcf

i don't know what -D read depth means in

i am having 101245 reads FYI.
ketan_bnf is offline   Reply With Quote
Old 07-28-2011, 06:54 PM   #2
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Location: hongkong

Join Date: Jul 2011
Posts: 1

The -D option of varFilter controls the maximum read depth, which should be adjusted to about twice the average read depth.
Shambala is offline   Reply With Quote

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