On Fri, Aug 3, 2018 at 2:30 AM James Bonfield wrote:
> On Thu, Aug 02, 2018 at 02:44:39PM -0400, Thomas W. Blackwell wrote:
> > The problematic feature is this: if the header of the existing .bam
> > file already contains md5 checksums in the "@SQ" header lines for
> > the individual hg19 sequen
On Thu, Aug 02, 2018 at 02:44:39PM -0400, Thomas W. Blackwell wrote:
> The problematic feature is this: if the header of the existing .bam
> file already contains md5 checksums in the "@SQ" header lines for
> the individual hg19 sequence contigs used in read mapping, then
> samtools will copy thos
Ziga -
In my experience, the .cram format is engineered to support this, but the
samtools software has one feature which causes all kinds of trouble with
it.
The problematic feature is this: if the header of the existing .bam file
already contains md5 checksums in the "@SQ" header lines fo
