Depth of Coverage for all SNP in reference genome in a BAM file

Question

[jingning629]

Hello!

I'm new to this area. Sorry in advance if I say something inaccurately.

Now I have Raw Sequencing Data for many samples, and also a reference genome. For a given sample, I want to find out the depth of coverage (the number of reads that cover a given nucleotide) for all positions of SNPs in the reference genome. Is there any tools that I can use? I found that I can know the Read Depth using GATK HaplotypeCaller but only for the nucleotide having variants (genotype 0/1 or 1/1), which is lack of information for the 0/0 genotype.

Thank you in advance!

[finswimmer]

Hello,

have you already mapped and aligned you reads to your reference genome? What genome is it? What do you mean by "for all positions of SNPs in the reference genome"? If you want to know the read depth on position where your sample has a variant, just do a variant calling. In the resulting vcf file there should be that information.

fin swimmer

Answer 1

[Bastien Hervé]

Maybe not the fastiest way but you can download the dbSNP of your reference genome.

Create a bed file with chromosome names and positions from your dbSNP.

Use samtools depth with option -b (with a specific bed file) on your bam file.

[jingning629]

Thank you! I didn't find a dbSNP file with my reference genome. The reference genome is just a .fa file. Could I generate the dbSNP using it?

[Bastien Hervé]

You need to provide some complementary informations. What is your reference genome, which version. Where did you get it (Gencode, Ensembl...) ?