Large *.bam files difficult to open in UGENE

Question

[Askhat]

Hello everyone!

I have a .bam file and bai file.

.bam file's size is 13.8 Gb. I attempted to open it in UGENE in order to see what's inside (reference gene sequence, in this case it's CYP2D6, and reads mapped to it), but the loading starting from 50% (cause I created bai file via samtools index before that) only proceeded to 56% in 5 hours and eventually got stuck.

I have the following PC specs:

• Processors: 8 × Intel® Core™ i7-4810MQ CPU @ 2.80GHz
• Memory: 23,1 GiB of RAM
• Graphics Processor: Mesa DRI Intel® HD Graphics 4600
• Graphics Processor: Quadro K1100M

Honestly, I have no idea how to open this file and see the reads aligned. Is there any idea what to do with the *.bam file in order to make it smaller? Is there any way to "reduce the depth of the reads"? I assume this is why the file is so big.

What I mean by the depth of the reads is pretty much the coverage depth, or the number of reads going deeper (shown on the screenshot below)

[Pierre Lindenbaum]

How about 'just' using IGV ?

[Askhat]

Thank you for suggestion! I will try it out

[Pierre Lindenbaum]

Is there any idea what to do with the *.bam file in order to make it smaller?

samtools view -o subset.bam -O BAM indexed.bam "chrom1:234-567"

Is there any way to "reduce the depth of the reads"?

samtools view with option -s (Subsampling shorthand option)

[Askhat]

Thank you very much, Pierre!

This is a very helpful info.