Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
small .bam files to test GATK Variant Discovery pipeline
Could someone refer me to where I could download the smallest possible .bam files to test my GATK Best Practices Variant Discovery pipeline? My pipeline uses the -L option to parallelize over different chromosomes - I would like to test this functionality and so I would like a full .bam file that has data from all chromosomes and will not cause GATK to crash.
I recieved this recommendation: Just use any BAM that you have on disk, make a little BED file with one interval per chromosome, e.g. chr1-22 from 6000000-6100000 respectively, and use SAMtools view to get a subset of the whole BAM:
samtools view -bh -o out_subset.bam input.bam -L regions.bed, however this caused GATK to crash. Any help here would be much appreciated. Thanks!