filter Refseq file with bed? to produce coverage per gene
Hi I am using GATK DepthOfCoverage -genelist mode to find the coverage per gene. The output contains many 0 coverage for genes that are not in the panel. Can I fix it by removing the genes that are not in the bed file ? Could you suggest a way to do this please?
Thank you
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Decrease in the read depth of the sample after Mutect2
written by kamanovae •
-
liftover bed not matching panel gene names
written by whb •
-
DepthOfCoverage Error: no suitable codec found
written by whb •
-
Post Alignment basic QC of RNA-Seq data
written by daewowo •
-
Refseq file 0 coding length
written by whb •
-
How to force GATK haplotypecaller to output all genomic position (even non variant positions)
written by Nicolas Rosewick
-
Using Bedtools coverage to find BAM coverage?
written by vctrm67 •
-
Problem: GATK insallation
written by whb •
-
Coverage analysis in a targeted amplicon-based next-generation sequencing panel
written by armarkes •
-
GATK-Depth of Coverage - Issue with per gene coverage
written by ttom
