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elcinchu27 ✭
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- elcinchu27
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Comments
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@birger I only checked for typos, so that is the original configuration of the method. There are some analysis launched with MutationCalling_QC_v1-1_BETA_cfg too.
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Thank you @Geraldine_VdAuwera, I dind't see that I have made the question in the wrong place, sorry for that,
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Hello @birger, I have already shared the workspace with you. I used the 1271 pair for all the trials, if you need something else just tell me.
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Hi @birger, again, After one week the problem remains the same. Please, could you tell me if my problem is common or not and how could I fix it? Maybe your method in "Broad_MutationCalling_QC_Workflow_BestPractice" is not the best practis…
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I just checked the input and output files of "PrintReads" with "-DBQ 20" and I don't see any difference between them, because the asterisk is still in the new bam generated by the program. I don´t know why there is no change betw…
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Yes, I looked for errors and warnings but the output shows "No errors found": /usr/lib/jvm/java-1.8.0-openjdk-amd64/bin/java -Xmx2g -jar /opt/picard-tools/picard.jar ValidateSamFile \ I=input_bam \ OUTPUT=output_errors.lis…
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Hello again @Geraldine_VdAuwera, As you said, I tried to add flat default values for the qscores but unfortunately I still have the same problem with the pipeline: java -jar /usr/local/bin/GenomeAnalysisTK.jar \ -T PrintReads \ …
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Hello @Geraldine_VdAuwera I am not sure but I think that I have the "asterisk problem" with CollectMultipleMetrics in the "MutationCalling_QC_v1-1_BETA_cfg" pipeline: -INFO 2017-03-09 17:42:01 SinglePassSamProgram Processe…
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@shlee great! Thanks a lot.
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Ok, I could do that with Samtools I think. But the problem is that I have the files in the cloud and the size of a whole-genome BAM is really large, so it could be really interesting that in the future this problem could be resolved. Thank you for …
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I have the same problem with my conversion from CRAM to FASTQ files. The Picard version that I used is the last one 2.9.0 and I provide the reference sequence too.
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When I use the LENIENT value I do not have any problem but when I use the STRICT default value in VALIDATION_STRINGENCY, I have this error: [Mon Feb 13 22:28:58 UTC 2017] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 36.17 minutes. Runtime.…
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You are right, the original bam is truncated too and I do not know why. It is my first experience with this pipeline and I thought that there was something wrong with my script. I have never seen a truncated read in a bam before so sorry for that. …
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The problem is that the lengths of reads that I input differe from the resulting reads that I have in the fastq. All the reads should be of 76 bases, but in the 001ND_2.fastq they only have 39.
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I have written this pipeline in firecloud but I have a problem with the fastq files, because the first fastq has reads of 76 bases while the second one has 39 bases. Could you explain what is the problem with the outputs? 001ND_1.fastq: @HWUSI-EAS1…
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I think that it would be more time-saving if all the intermediate files were automatically removed in the end of the workflow.