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- Richard Thompson
Hi Sheila, The file has been uploaded: biscuit13161_sp13.tar.gz I've included the slightly modified ucsc reference and the bed file that I'm using as well as the stack for both the original and the snippet runs. The snippet includes the entire ge…
Hi Sheila, sorry, I should have been clearer - GATK is reporting that no other filters are filtering out any reads: INFO 14:01:45,101 ProgressMeter - Total runtime 6542.25 secs, 109.04 min, 1.82 hoursINFO 14:01:45,102 MicroScheduler - 7043281 re…
Hi Geraldine, Thanks for your response. FYI, I just wanted to let you know that I've been in contact with the Novoalign developer and this morning he has released an update (NovoalignCS V1.03.05) which includes a limit on the quality scores of 60, …
Hi Geraldine, I apologise, I didn't phrase my question very well. ... and yes the information in that article will be helpful, I have no doubt. However as I'm also using novoalign and I've been assured by the programmer that it outputs using Phred3…
Hi, As I've just come across this issue with my own files, could you explain how you were able to see that "sample1.lane1.novoalignCS.sorted.MarkDups.nRG.Real.chr12.bam has misencoded quality scores"? Thanks, Richard
Sorry, allow me to clarify myself. The BAM input data has no chrM at all. This issue is occuring even when using the unmodified reference and unmodified VCF files from the GATK-Bundle.
Apologies, the log file isn't very readable in my question so I've attached it here
Hi Geraldine, Obviously I don't know about Pallavi, but I do know I'm observing this with v2.5.2.
following on from this, can you explain why the number of processed reads ( "INFO 02:09:56,512 BaseRecalibrator - Processed: 1059663038 reads" from Pallavi's example) differs so much from the total number of reads ("INFO 02:09:56,514 …