What is the common practice to view WGS data on IGV?

Question

[chictu]

Hi,

I would like to manually examine mutations on specific chromosomes in around 50 whole-genome sequencing (WGS) data samples. Each BAM file is larger than 10GB.

I'm wondering about the standard approach for visualising these mutations using the IGV. My concern is that downloading all the BAM files might lead to storage issues, as well as the wastage of time and resources. Considering I'm only interested in 2 to 3 chromosomes within each BAM file, is it reasonable to think that there might be a more efficient way to accomplish this?

Thanks!

Answer 1

[barslmn]

There is this great repo igv-reports. It makes it really easy to look at variants and the alignments together. If you have a subset of variants it's going to retrieve alignment related to those.

Answer 2

[rfran010]

Where are these bam files stored? And are you able to work with them on the command line?

If you can work with them before downloading, you can derive the reads from your region of interest using samtools. Otherwise, you can see if you can upload to IGV via a URL.

At the very least, you could download, sample your region, and then delete and work on the next one.

[chictu]

they are on the HPC. ok I will try subsetting the BAM files with samtools before downloading. Thank you!

Answer 3

[liorglic]

If you are interested in mutations, then you might consider performing some variant calling procedure on the BAM files. This will result in a VCF file, which you can then view in IGV (it is much lighter than BAMs).