Gene specific region visualization in Alignment (.bam) or Variant calling file (.vcf) in IGV

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9.3 years ago

ravi.uhdnis ▴ 220

Hi,

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.

Assembly alignment genome SNP next-gen • 3.7k views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by ravi.uhdnis ▴ 220

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

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by GouthamAtla 12k

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