How to get the coverage of whole gene in exome sequencing data
I can get the allelic depth of any SNP by using pile-up. However, I need to get the coverage of gene in the exome sequence (preferably with number of reads with REF allele and number of reads with ALT alleles). I have some genes where variants are not called by GATK and I want to check if that is because of low coverage and not because they do not exist. Is there a way to do this using BAM files rather than going through each individual gene using IGV?
2 answers
See samtools bedcov or samtools depth.
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Sean Davis
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