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rcorbett

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Latest activity by rcorbett
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    rcorbett created a post,

    GATK-DRAGEN standalone pipeline?

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    1. Community
    2. General Discussion

    Hi folks, I have been asked to try out your GATK-dragen pipeline.   I found this and related pages: https://gatk.broadinstitute.org/hc/en-us/articles/4411716682011-Full-release-of-open-source-DRAGE...

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    rcorbett commented,

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    3. CollectRnaSeqMetrics GL000220 test not counting ribosomal reads

    OK.  I think we're making some progress here.   I am starting with a refseq .gtf file where the annotation for my rRNA looks like this: chrUn_GL000220v1 BestRefSeq transcript 105424 118780 . + . ge...

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    rcorbett commented,

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    3. CollectRnaSeqMetrics GL000220 test not counting ribosomal reads

    Many thanks for your help Genevieve Brandt (she/her). It is more that I am confused by the output.  I am not expecting a high UTR amount as my data are almost exclusively ribosomal and 45S, to my k...

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    rcorbett created a post,

    CollectRnaSeqMetrics GL000220 test not counting ribosomal reads

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    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: gatk-4.1.9.0 b) Exact command used: gatk-4.1.9.0/gatk CollectRnaSeqMetrics -I A56781.STAR.genome.sorted.bam.dup.bam.chrU...

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    rcorbett commented,

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    3. filterSamReads stdout format error

    OK. I uploaded a file called filterSamReads_output_format.tar.gz I was surprised to not be asked for a password at the following address, so it might be worth checking if the file is in fact on you...

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    rcorbett commented,

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    3. filterSamReads stdout format error

    Thank you. I tried the same command with 4.1.9.0 and got the same errors.  I will create a bug report.

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    rcorbett commented,

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    3. filterSamReads stdout format error

    Good afternoon. gatk ValidateSamFile -I passed.bam   -M SUMMARY Summary output: ## HISTOGRAM java.lang.StringError Type CountERROR:MISMATCH_FLAG_MATE_NEG_STRAND 14964150WARNING:ADJACENT_INDEL_IN_CI...

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    rcorbett commented,

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    3. filterSamReads stdout format error

    Hi Genevieve Brandt (she/her), For 1. above:gatk PrintReads -I stdout.bam -O tmp.tmp --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true'Using GATK jar /gsc/software/linux-x86_64-centos6/gatk-...

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    rcorbett commented,

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    3. filterSamReads stdout format error

    Hi again, we tried the same command on a BWA 0.7.6a mem aligned bam and ran in to the same issue.

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    rcorbett commented,

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    3. filterSamReads stdout format error

    Thanks Genevieve, If I looks through the file I don't see anything human readable.  Similarly, if I try  strings stdout.bam I don't see anything of note. Just a little more information on the above...

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