Hello, I have code that indicates there are a number of SNP mutations at specific locations for different cell types and none for others. I need to align all the respective long reads at that coordinate to see if my code works. These BAM files are located on a remote server and are too large for me to download them locally to my computer. I am really stuck, can anyone help me out? It is my first time doing this and I've never used IGV before. Happy to answer any questions that might help clarify what I need.
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bxxxmxxxx •
if the remote server supports random access, you can use "load from URL": https://software.broadinstitute.org/software/igv/LoadData
otherwise, you could download only a part of the bam:
wget -O - "http://path/to/in.bam" | samtools view -O BAM -o subset.bam -L regions.bed && samtools index subset.bam
Sorry to be a noob, but what does the -L region.bed do? As in could you provide an example? I feel in over my head.
the manual is available here: http://www.htslib.org/doc/samtools-view.html
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