Question: Calculating coverage on a list of individual genes in WES data?
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gravatar for gvelz
2.3 years ago by
gvelz0
gvelz0 wrote:

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?

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by gvelz0

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?

ADD REPLYlink written 2.3 years ago by gvelz0

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

This comment belongs under @trausch's answer.

ADD REPLYlink written 2.3 years ago by genomax84k

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.

ADD REPLYlink written 2.3 years ago by genomax84k

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.

ADD REPLYlink written 2.3 years ago by trausch1.5k
1
gravatar for trausch
2.3 years ago by
trausch1.5k
Germany
trausch1.5k wrote:

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.

ADD COMMENTlink written 2.3 years ago by trausch1.5k
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