Thomas Keane

Sorry, I assigned blame to the wrong command. It is actually 'samtools merge' that caused the crash e.g. samtools merge out.bam /lustre/scratch107/projects/pombe_jeffares/external_lane_bams/jb874.bwa7a.sort.bam /lustre/scratch107/projects/pombe_jeffares/sanger_lane_bams/1996STDY5244977/4858070/7816_3#80.bam [bam_merge_core] different target sequence name: 'mito' !=...

Hi - currently mpileup is not multi-threaded. What people usually do is to break the genome into regions and run them in parallel. We will add this request as a...

I suspect that your exonerate alignment did not complete. This line is where it checks the exonerate output for "-- completed exonerate analysis" from exonerate to say it completed fully....

Hi - I just re-ran the NA12878 data from the wiki page and it completes just fine. The underlying cause is usually that exonerate ran out of memory, if you...

Yes, that is correct. But to be honest, I never consider the breakpoints to be accurate to the exact bp. Some mini local assembly and realignment could get them to...

Can you post the command that you ran?

Hi - can you grab the latest release that I just made and try it. That should solve the problem. Let me know if not. Thomas

Hi All - it has been quite a few years since I looked at the code. As a workaround, can you use the -chr parameter to call on the autosomes...

Can you provide the command lines you have run? On 20/04/17 22:01, lokeyCEU wrote: > > I have merged .bam files from the 1kGP (with samtools merge -r) and >...

Hi, Is samtools available in your default path? i.e. what happens if you just type 'samtools' on the command line, is it found? Rgds, Thomas On 04/04/16 13:32, Emma-Drieux wrote:...