On Thu, 28 Aug 2014 16:36:11 -0400
Nils Homer wrote:
> Could it be because we search for the associated sequence dictionary
> using the fasta file name, and the dictionary it finds for one is
> missing or mismatching? You could search for *.dict or *.fai files
> for each path.
Right again. It's
Could it be because we search for the associated sequence dictionary using
the fasta file name, and the dictionary it finds for one is missing or
mismatching? You could search for *.dict or *.fai files for each path.
N
On Thu, Aug 28, 2014 at 3:50 PM, Jeremy Volkening
wrote:
> Well, that did
Well, that did the trick. I had given up on providing the reference
sequence because it always crashed picard with:
Exception in thread "main" java.lang.NullPointerException
at
htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:87)
at
picar
Try giving it a reference sequence (R=...) to see if the alignment-based
metrics are output.
N
On Thu, Aug 28, 2014 at 2:35 PM, Jeremy Volkening
wrote:
> Hello,
>
> I have a set of ~ 1 billion gDNA paired reads mapped to a reference
> genome with BWA-MEM. I tried to use picard's
> CollectAlign
