sequencing data from different samples in the Integrative Genome Viewer (IGV)

Question

[José de la Trinidad]

Greetings, I need to carry out an activity for my master's degree in Biostatistics and Bioinformatics that consists of viewing sequencing data from different samples in the Integrative Genome Viewer (IGV) in order to analyze alignments and variants.

I MUST

1. Select and, if necessary, download the corresponding human reference genome and upload it to the IGV. Subsequently download and load the alignment data of two samples to be studied. Verify the sequencing depth of that region.
2. Locate a selected gene from a bibliographic reference and locate a possible variant. Attach an image
3. Verify if the selected variant is true or is due to some error during sequencing or incorrect alignment. Justify the answer based on some criterion such as sequencing depth or the quality of the reads.

The problem is that I don't know how to download the gen or the .bam file I need. If anyone can help me. Thank you.

Jose from Venezuela

mail: [e-mail]

[rpolicastro]

Generally we don't provide answers for assignments here. As a very generic hint you can download the human reference and variants from places like NCBI or ENSEMBL.

Also I edited out your email since it's usually safer not to include it due to reasons of e.g. phishing and spam.

Answer 1

[DKA]

Check out their documentation on the official IGV website. There is also a YouTube channel for IGV that can be a good start.