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biocc

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Join Date: Jul 2008

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why use -D in samtools

10-20-2010, 03:07 AM

to call snp and indels, in FAQ of samtools , it gives
samtools pileup -vcf ref.fa aln.bam | tee raw.txt | samtools.pl varFilter -D100 > flt.txt
awk '($3=="*"&&$6>=50)||($3!="*"&&$6>=20)' flt.txt > final.txt

why use -D and how to determine it
i think the higer depth, mutation will be more credible.
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