User: marcosp

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marcosp0
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Posts by marcosp

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Issue with Realign Indel
... After trying the "ReorderSam" tool, I get this message:   Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch Exception in thread "main" picard.PicardException: New reference sequence d ...
written 2.5 years ago by marcosp0
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Issue with Realign Indel
... So I have gotten to the point where I'm realigning indels, and had my reference file (hg19) uploaded into my history into the workflow, then then following message shows up: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch [Thu Oct 15 22:26:17 CDT 2015] net.sf.picard.sam.CreateS ...
realign indel written 2.5 years ago by marcosp0 • updated 2.5 years ago by Jennifer Hillman Jackson24k
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Comment: C: How to Realign Indels and logic of workflow
... Thank you! Another question, I have heard of people merging their data. Is this specific to multiple reads on one sample, or should it be done on all samples (i.e. a trio being analyzed for variants). In a Galaxy tutorial, the person merged all of the samples after mapping them, but I don't know if ...
written 2.5 years ago by marcosp0
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Comment: C: Realigner Target Creator in GATKtools
... I posted this in the general forum, since it is a new question.  ...
written 2.5 years ago by marcosp0
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How to Realign Indels and logic of workflow
... I have paired end reads of a trio that I eventually need to call variants on (make a .vcf). So I'm experiencing the same thing. Please tell me if my logic is correct: FASTQ->FASTQC->BWA-MEM (Read group ID assigned as part of this step) -> Sort with SAM Tools -> Filter -> Clean ->M ...
realign indels workflow gatk tools written 2.5 years ago by marcosp0 • updated 2.5 years ago by Jennifer Hillman Jackson24k
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Answer: A: Realigner Target Creator in GATKtools
... I have paired end reads of a trio that I eventually need to call variants on (make a .vcf). So I'm experiencing the same thing. Please tell me if my logic is correct: FASTQ->FASTQC->BWA-MEM (Read group ID assigned as part of this step) -> Sort with SAM Tools -> Filter -> Clean ->M ...
written 2.5 years ago by marcosp0

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