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!