Calculating coverage on a list of individual genes in WES data?
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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>
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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?
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ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized.This comment belongs under @trausch's answer.
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.
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.