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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Can't see realigned bams in the latest IGV on windows #246

Closed waalkes closed 2 years ago

waalkes commented 2 years ago

I have tried to load the realigned bam in the latest IGV (2.14.1) on Windows and the initial(input) bam works but the realigned bam (command line below) nor the sorted (I tried sorting it) show anything. The reference is CP034067.1

docker run -v /mnt/disk4/labs/salipante/databases/reference_genomes/$ref:/mnt/disk4/labs/salipante/databases/reference_genomes/$ref -v /mnt/home/waalkes/shigella3/$pfx.Analysis:/mnt/home/waalkes/shigella3/$pfx.Analysis docker.labmed.uw.edu/docker-images/octopus:v0.7.4-63d80f00 octopus -R /mnt/disk4/labs/salipante/databases/reference_genomes/$ref/$ref.fa -I /mnt/home/waalkes/shigella3/$pfx.Analysis/$pfx.shortread_genome.bam -P 1 --threads 64 -o /mnt/home/waalkes/shigella3/$pfx.Analysis/$pfx.octo_bamout.vcf --bamout /mnt/home/waalkes/shigella3/$pfx.Analysis/$pfx.realigned.bam

Am I missing something?

Thanks

waalkes commented 2 years ago

Fixed. I updated and sorted and indexed with a later version of samtools and it worked.