Hi all, I have a very fragmented reference genome (>million scaffolds) that I was able to call variants using Samtools-mpileup V0.19. However, V1.1 hanged on the same data set with no error produced, just never run to completion. The V1.1 still does not work if I extract alignments on a small subset of scaffolds, however, it will work if I also re-header the sub-bam files. Is there anyway to increase the maximum allow scaffolds in the header? Thanks.
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