Calculating coverage on a list of individual genes in WES data?

Question

[gvelz]

I have whole exome sequencing VCF and CRAM files from a few human samples and would like to calculate the sequence coverage on a list of individual genes. Is there a good way to go about doing this?

[gvelz]

Thanks! I installed Alfred, but am unsure how to make a list of genes in .bed format. Also, does this program work for .cram files?

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This comment belongs under @trausch's answer.

[GenoMax]

You should be able to get a BED format gene list following this: How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols

Choose the genome build you are interested. Rest of the directions should work.

[trausch]

I recently added cram support. If you clone the github repository there is an example Rscript that downloads ccds genes from UCSC and stores all exons in a BED file.

Answer 1

[trausch]

If you want a fragment count table for these genes you can use Alfred:

alfred count_dna -o cov.tsv.gz -i genes.bed <input.bam>

For estimating the on-target rate and the avg. coverage per target region:

alfred qc -b genes.bed -o qc.tsv.gz -r <genome.fa> <input.bam>

Static binaries are available here or via Bioconda.