Question: How To Interpret -D File In Samtools Variant Calling Pipeline?
1
gravatar for Ian
9.9 years ago by
Ian5.7k
University of Manchester, UK
Ian5.7k wrote:

I have been using using the samtools pipeline for variant calling for a while now and have just moved over to using mpileup. I am using the suggested method:

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

I am aware at the vcfutils step that '-d' specifies the minimum read depth and '-D' specifies the maximum read depth. However, what is not clear to me is, for example, if -D = 100 and the coverage of a SNP is 200, what happens? Do 100 random reads get used, or more worryingly is that SNP not reported?

Thanks.

samtools vcftools • 4.1k views
ADD COMMENTlink modified 9.9 years ago by Farhat2.9k • written 9.9 years ago by Ian5.7k
5
gravatar for Farhat
9.9 years ago by
Farhat2.9k
Pune, India
Farhat2.9k wrote:

From the source code it appears that the SNP is not reported if the coverage exceeds the maximum depth.

ADD COMMENTlink written 9.9 years ago by Farhat2.9k
2

Farhat gives the correct answer.

ADD REPLYlink written 9.8 years ago by lh332k

I have reopened this questions as it is crucial whether a SNP uses sampled reads or is skipped if coverage is above -D. Thanks for your effort Farhat, but 'appears' is not definite enough.

ADD REPLYlink written 9.8 years ago by Ian5.7k

Thanks for the confirmation, Li. I had only taken a cursory look so didn't want to be too certain of the answer.

ADD REPLYlink written 9.8 years ago by Farhat2.9k

My understanding is that if unique or "reliable" (from FAQ of samtools ) sequences are used for snp calling, the -D option is meaningless, since the high coverage is not caused by duplication of genome segments.

ADD REPLYlink written 8.5 years ago by C Shao130
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