dcampo ·

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dcampo
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  • @alanhoyle So I tried re-running with the --merge-input-intervals option, and it ran in literally 1 min... From weeks to 1 min!!! That option should really be emphasized in the tool description, or maybe even included by default. Thanks a lot!
  • @jcx9dy I did not have time to troubleshoot, so I ended up installing a previous version of GATK to avoid GenomicsDBImport. At some point I will have to come back to this and play around a bit with parallelizing, etc. That said, I don't believe it …
  • Oh, yes, that's the issue...it's running now. I knew it had to be something silly, but could not see it. Rookie mistake :) Thanks!
  • Hi, thanks for your reply. Here's my command line: java -jar $GATK ModelSegments \ --denoised-copy-ratios ${name}_dir/${name}_CTC.denoisedCR.tsv \ --allelic-counts ${name}_dir/${name}_CTC_clean.allelicCounts.tsv \ --normal-allelic-count…
  • Hi, an update on my comment about "Syntax error in JSON file /tmp/loader_2075782628441988593.json". I specified a different temp folder, and I am not getting that error anymore. I guess the default temp folder was filling up quickly. Any…
  • Hi, I am having the same issue, and don't know how to fix it. Attached there's a snippet of the sample file. Thanks!
  • Hello! I am trying to run GenomicsDB, but after 12 h, it exits with the following error: terminate called after throwing an instance of 'GenomicsDBConfigException' what(): GenomicsDBConfigException : Syntax error in JSON file /tmp/loader_207578…
  • Well, if this helps, I have now implemented GATK4 for all the GATK part of my pipeline, and it run smoothly, with no issues. :smile: I have also run Mutect2 for somatic calling, and VEP for annotation afterwards, and everything looks fine. Thank …
  • Hi, an update on my previous comment (see right above): I just ran GATK4 - SplitNCigarReads on a small sample I am using for troubleshooting, and I only get a minor warning: WARNING:MISSING_TAG_NM 721424 No more ERRORS :) (Remember, when I ran …
  • Hi again! So I ran now ValidateSameFile on all bam files generated in the pipeline, and the output bams of STAR, Picard AddOrReplaceReadGroups, and Picard MarkDuplicate show no errors. The errors appear after SplitNCigarReads, and they are the same…
  • Thanks for the answer Geraldine, but I see there is some confusion here. I probably did not explain my self clear enough. Sheila asked me to validate the original bam files that I used for the analysis, and that's what I did. So the the bam files th…
  • Thanks Sheila, Yes, I had read that article before. That's why I am now running ValidateSamFile in all my bams. So, if I understand correctly from what Geraldine says in the second thread ("Some of these mapping issues can't be fixed as such, …
  • Hi, On the line of the above thread, I am doing somatic calling using RNAseq data, with matching tumor and normal samples. I have followed the Best practices recommendations for RNAseq pre-processing, all the way to re-calibrated bam files. Then, u…
  • HI Sheila, an update on this: I ran ValidateSamFile on all the 91 bam files I am using in this analysis, and for 77 of them I get the error mentioned above (ERROR ValidateSamFile Value was put into PairInfoMap more than once. -1: READNAME_here). T…
  • Yes, those are bamouts from Mutect2. I have checked the 4 bam files that were used for those two Mutect2 runs (i.e. 2 tumor-normal pairs) with ValidateSamFile, and they all yield the same error: ERROR ValidateSamFile Value was put into PairInfoM…
  • I just ran it quickly on a couple of the bam files, and got very similar results: Error Type Count ERROR:MATES_ARE_SAME_END 115868 ERROR:MATE_NOT_FOUND 1049691 ERROR:MISMATCH_FLAG_MATE_NEG_STRAND 231736 ERROR:MISMATCH_MATE_ALIGNMENT_START 75…
  • Hi again, Turns out that MergeSamFiles does not accept a list of bams :( And when I tried entering manually the names of the 25 files, it quit with the error "SAM validation error: WARNING: Read name READNAME, No M or N operator between pair…
  • Thanks Sheila! One last thing thing, I have 25 bam files per sample (one per chr), so I assume I can pass a list of input files, like for CatVariants and many other tools? Something like: I=listofbams.list
  • (Quote) Hi Sheila, Following up on this, is it OK to use a PoN created with MuTect2-GATK3 for somatic variant calling with Mutect2-GATK4? Thing is, my entire pipeline for somatic calling with RNAseq is based on STAR-GATK3, but when running MuTect2 …
  • Hi again, I plotted the read counts, but I don't see any clear regions of high coverage. There are just a few genes with more coverage than the rest, but they are not concentrated in any particular area. Besides, I see that same pattern (with very …
  • Hi again Geraldine! I finally got a chance to try qualimap. However, it gets stuck at 39%, which I am guessing is where the bam reaches the high coverage region. Maybe it's a (lack of) memory issue, but at least in my laptop, it won't go past that 3…
  • Thanks for the help, Geraldine! I tried to load the sample in IGV, but it's not helping much. What program would you recommend? Thanks!