Question: Gene specific region visualization in Alignment (.bam) or Variant calling file (.vcf) in IGV
gravatar for ravi.uhdnis
4.9 years ago by
United States
ravi.uhdnis180 wrote:


I have multiple whole genome alignment files (.bam of a human sample) and also have one variant calling file (.vcf) generated using GATK HaploTypeCaller, using reference genome GRCh38. I can visualize them in IGV as "chromosome no. wise" but unable to view "GENE name" wise i.e. IGV doesn't show me the aligned/mapped regions of .bam files whenever i enter any gene name in search box e.g. EGFR, HLA-DRB1 etc. It simply display box with message "Cannot find feature or locus: gene name". I want to see alignment files reads as well as subsequent SNPs/variations in .vcf file according to particular gene names. It would be great if somebody suggest me how to do that. thanks, Ravi.

ADD COMMENTlink modified 4.8 years ago by Biostar ♦♦ 20 • written 4.9 years ago by ravi.uhdnis180

You could enter the gene coordinates. There is an option called GeneListView which might help you.

ADD REPLYlink written 4.9 years ago by geek_y11k
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