PeteHaitch · ✭
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- Peter Hickey
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Thanks, Geraldine. That's indeed what I was asking. It might be worth noting that in the documentation.
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Are the .chain files different to those provided by the UCSC genome browser, e.g. http://hgdownload.cse.ucsc.edu/goldenPath/mm9/liftOver/mm9ToMm10.over.chain.gz? If so, are you able to make the mm9 to mm10 files publicly available? Thanks
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(Quote) ggplot2 isn't a part of core R. It must be installed separately via install.packages(“ggplot2”)
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@ivernar - This sounds like the same error I encountered. I'm still unable to produce the BQSR plots automatically despite changes made from v2.0 to v2.1. My fix is to add the -k flag to my call to BaseRecalibrator (to retain the temporary csv file)…
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Hi Geraldine, I'm thinking of options like in VariantFiltration, e.g. --filterExpression "AB < 0.2 || MQ0 > 50". I doubt I'll have time myself to implement such a thing but I thought I'd raise it here in case it was something of int…
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My apologies for my stupid mistake. Fixed up the typo and it works as expected. Thanks.
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@pdexheimer Thanks! That's just the sort of advice I was looking for regarding which strains of the Keane paper to retain. It's certainly looking the easiest option currently. A couple of minor things that you may need to be adjust before this can b…
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I'm currently dealing with this issue in mouse. I'm using mm9/MGSCv37 because there seem to be more resources available for this reference than the latest mm10 build. There are a few databases of variation that I am trying to choose between: * dbSN…
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Just to confirm, it was a problem caused by lack of space in my tmp directory. Re-running the command with a different tmp directory worked.
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Okay. Two follow-up questions: * How do you at the Broad deal with BWA not complying with BAM spec (e.g. "MAPQ value should be 0 for unmapped read") * Why does ReduceReads seem to work on a BAM containing only those 4 reads that violate B…
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No, the BAM does not pass ValidateSamFile. See the attached log file for errors raised by it. The BAM was generated using BWA and then following GATK Variant Detection Best Practises v4. I extracted the reads that failed ValidateSamFile and tried ru…
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Pardon my ignorance, but is the stack trace the log output? I've attached the log file from one of the BAMs. Please let me know if this isn't what you need.
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No problem, Mark. One further improvement would be in the labelling of the x-axis tick marks for the "context covariate plots" - the three base suffixes are basically illegible in the plots I've seen.
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I've found the problem and it's due to changes in ggplot2 for version >=0.9 and a missing grid package in R. Specifically, in BQSR.R the following is called: scale_y_continuous(formatter="comma") This will work for version < 0.9 of…
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Thanks for the pdf, Ryan. I think I've figured out the problem. I am using GATK v2.0 (Beta) (v2.0-39) downloaded from http://www.broadinstitute.org/gatk/download and this does not include the BQSR.R script. As far as I can tell, BQSR.R is only incl…
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Hi Ryan, Hmm, the plot thickens. I re-ran BaseRecalibrator and still did not get a pdf plot, however the error message changed. Both attempts to use the BaseRecalibrator were using the entire BAM (i.e. not using Eric's trick). Here is my command l…
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I've rerun BaseRecalibrator with the `-l DEBUG' flag. Here is (I think) the relevant output: INFO 08:20:48,388 BaseRecalibrator - Generating recalibration plots... DEBUG 08:20:48,827 RScriptExecutor - Executing: DEBUG 08:20:48,827 RScriptExecuto…
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I can confirm that Rscript is in my path. I'll need to re-run BaseRecalibrator in order to get the log as I foolishly didn't save it to file. I'll post that once I have done so. Cheers unix303 507 % echo $PATH/usr/local/bioinf/bin:/cluster/home/us…