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asebastian 03-31-2013 08:53 PM

Variant Calling with mpileup
Hi all,

I am a new bee to variant calling. I am using samtools mpileup. My criteria includes:
-- minimum total coverage of 5
-- minimum variant-supporting coverage of 2
-- minimum average base quality of q15
-- minimum variant allele frequency of 0.01

This is how I am doing it

samtools mpileup -DS -C 50 -m 2 -F 0.01 -Q 15 -f ref.fa test.bam | bcftools view -bvcg - >test.bcf

bcftools view test.bcf | varFilter -d 5 >test.vcf

Is this the way to do it?

Also how do I find "mean position of the variant within the variant-supporting reads" ?

Thanks in advance for all your comments and suggestions.


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