Question: Calculating Sequencing Depth Of A Genomic Region
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gravatar for User 1933
6.6 years ago by
User 1933340
User 1933340 wrote:

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 ?

vcf exome-sequencing • 3.2k views
ADD COMMENTlink modified 6.6 years ago by Alex Paciorkowski3.4k • written 6.6 years ago by User 1933340
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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).

ADD REPLYlink modified 12 months ago by RamRS30k • written 6.6 years ago by Biomonika (Noolean)3.1k
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gravatar for Alex Paciorkowski
6.6 years ago by
Rochester, NY USA
Alex Paciorkowski3.4k wrote:

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.

ADD COMMENTlink modified 12 months ago by RamRS30k • written 6.6 years ago by Alex Paciorkowski3.4k
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