[Samtools-help] large fragmented reference genome

[Koh, C. <Chu...@nr...>]

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.

With Regards,
Kevin Koh