Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: How To Interpret -D File In Samtools Variant Calling Pipeline?
1
gravatar for Ian
9.9 years ago by
Ian ♦ 5.7k
University of Manchester, UK
Ian ♦ 5.7k 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 COMMENT • link •
modified 9.9 years ago by Farhat • 2.9k • written 9.9 years ago by Ian ♦ 5.7k
5
gravatar for Farhat
9.9 years ago by
Farhat • 2.9k
Pune, India
Farhat • 2.9k wrote:

From the source code it appears that the SNP is not reported if the coverage exceeds the maximum depth.
ADD COMMENT • link written 9.9 years ago by Farhat • 2.9k
2

Farhat gives the correct answer.

ADD REPLY • link written 9.8 years ago by lh3 ♦ 32k

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 REPLY • link written 9.8 years ago by Ian ♦ 5.7k

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

ADD REPLY • link written 9.8 years ago by Farhat • 2.9k

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 REPLY • link written 8.5 years ago by C Shao • 130
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2432 users visited in the last hour
_