Question: (Closed) Help with GATK protocol
gravatar for eennadi
25 days ago by
eennadi0 wrote:

I wish to call variant using the GATK workflow. However, I am having problems

  1. Indel re-aligner. I am confused with this step "Restrict realignment to provided intervals". How do I get the GATK intervals I downloaded dbSNP from NCBI database in VCF format but

  2. Realigner Target Creator for use in local realignment; I get this error message.

INFO 10:34:18,285 HelpFormatter - --------------------------------------------------------------------------- INFO 10:34:18,287 HelpFormatter - The Genome Analysis Toolkit (GATK) vexported, Compiled 2014/03/19 14:39:06 INFO 10:34:18,287 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 10:34:18,288 HelpFormatter - Please view our documentation at INFO 10:34:18,288 HelpFormatter - For support, please view our support site at INFO 10:34:18,288 HelpFormatter - Program Args: -T RealignerTargetCreator -o /galaxy-repl/main/files/023/686/dataset_23686636.dat -et NO_ET --num_threads 1 -I /galaxy-repl/main/jobdir/018/449/18449237/_job_tmp/tmp-gatk-xZmTXk/gatk_input.bam -R /galaxy-repl/main/jobdir/018/449/18449237/_job_tmp/tmp-gatk-xZmTXk/gatk_input.fasta INFO 10:34:18,289 HelpFormatter - Date/Time: 2018/02/20 10:34:18 INFO 10:34:18,289 HelpFormatter - --------------------------------------------------------------------------- INFO 10:34:18,289 HelpFormatter - --------------------------------------------------------------------------- INFO 10:34:18,294 GenomeAnalysisEngine - Strictness is SILENT INFO 10:34:18,299 ReferenceDataSource - Index file /galaxy-repl/main/jobdir/018/449/18449237/_job_tmp/tmp-gatk-xZmTXk/gatk_input.fasta.fai does not exist. Trying to create it now. INFO 10:34:18,823 ReferenceDataSource - Dict file /galaxy-repl/main/jobdir/018/449/18449237/_job_tmp/tmp-gatk-xZmTXk/gatk_input.dict does not exist. Trying to create it now. INFO 10:34:19,696 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 10:34:19,808 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11

ADD COMMENTlink written 25 days ago by eennadi0

Hello eennadi!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


PS: Please see tutorial link in the related post for the most current variant analysis methods in Galaxy.
ADD REPLYlink written 24 days ago by Jennifer Hillman Jackson24k
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