Calculating Sequencing Depth Of A Genomic Region
In an whole-exome study project, I need to calculate the sequencing depth for a given set of genes. It seems DepthOfCoverage from GATK can do this for me. However, I am curious if I can get the similar information from the VCF file ? Alternatively is there any other tool I can use ?
• 6,647 views
•
link
updated
by
Alex Paciorkowski
•
written
by
User 1933 •
•
written
by
User 1933 •
1 answer
GATK DepthOfCoverage will give you want you want, but it takes bam files.
Also, read this, it's a nice discussion of using bedtools as well.
I wouldn't calculate my read depth across the target just using a vcf, since that file only includes your variant calls.
• 0 views
•
link
updated
by
Ram
•
written
by
Alex Paciorkowski
•
written
by
Alex Paciorkowski
Log in to answer this question.
More posts like this
-
Access to public exome files
written by storm1907 •
-
Calculating breadth of coverage for TCGA Whole Exome Sequencing data
written by steve
-
Calculating coverage on a list of individual genes in WES data?
written by gvelz •
-
MIN and MAX read depth for vcfutils.pl
written by nickmarinakis92 •
-
calculating LD-tools to calculate D' in DNA sequencing data with unphrased genotype
written by ren.yingxue •
-
PyClone without copy number data
written by Alejandro Jimenez Sanchez
-
Non-Coding Region On Hg19
written by User 1933 •
-
What Figure You Make For Qc Of Whole Exome Sequencing Data
written by User 1933 •
-
Webservice/Download Options For Homology Models
written by andreas.steffen •
-
What Genetic Marker To Use To Infer Pedigree From Sequencing Data?
written by michealsmith
As far as I know, VCF file will provide you depth only at the position of the variant. It depends if you are interested in depth at variants, average depth across the gene or in depth for every position in the gene. If the last one is your case, you can use "samtools depth" over the bam file (alignment file of reads over reference).