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3. erro running "gatk seq-format-validation workflow"

Hi Jason Cerrato  Thanks for your guidance. I changed the path in the Json file as you mentioned, unfortunately the workflow still fails. Please see files in the folder named" error gatk-workflows ...

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• zdr j
• August 06, 2020 11:04
• 1 vote

1. Community
2. Germline
3. erro running "gatk seq-format-validation workflow"

Hi Jason Cerrato  Thank you for your reply. Yes, the log folder is empty after the execution. And for the json file I tried with different formats and none of them worked. I added another json to t...

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• zdr j
• August 05, 2020 06:46
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• 1 vote

1. Community
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3. erro running "gatk seq-format-validation workflow"

Hello  Thanks for you help I tried many things with the json format and wdl, but the problem still exists. The link below has the files and folders for json, wdl and the input file I am using.    T...

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• zdr j
• July 31, 2020 07:43
• 1 vote

1. Community
2. Non-Human
3. Error Creatting Dictionary for genome

Hi Genevieve,  Well, as I explained before there is no roundabout step I am taking, the problem is that ICGC data that I am downloading are originally mapped by ICGC or illumina? to GRCh37 (hg19) a...

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• zdr j
• August 24, 2021 05:38
• 0 votes

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3. Error Creatting Dictionary for genome

maybe could not use a liftover tool (crossmap) and I had to realign my reads to hg38? like revert bam to fastq and then BWA MEM and ...?  

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• zdr j
• August 21, 2021 14:01
• 0 votes

1. Technical Documentation
2. Troubleshooting GATK4 Issues
3. Errors about input files having missing or incompatible contigs

Got the same problem, tried different references, did not solve the issue. frustrated at GATK Can any one introduce another software to call somatic mutations (small indels and point mutations) tha...

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• zdr j
• August 21, 2021 13:37
• 0 votes

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3. Error Creatting Dictionary for genome

Hi Genevieve, Thank you for your reply. I still have the problem. I think the problem is the reference hg38 file that I am using which I got from Broadinstitute Google bundle. It looks like it does...

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• zdr j
• August 21, 2021 09:22
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• 0 votes

1. Community
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3. Error Creatting Dictionary for genome

Thank you Genevieve, Picard worked to make the dict file. I used samtools to make the fai file. Now running mutect2, I still get this error which is similar to the error I got before when made dict...

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• zdr j
• August 06, 2021 10:12
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1. Community
2. Non-Human
3. Error Creatting Dictionary for genome

Hi Genevieve, Thank you for your help. This is the command I run and the error I get:  java -jar ~/picard-2.25.7/picard.jar CreateSequenceDictionary \       R=~/my_project/Homo_sapiens_assembly38.f...

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• zdr j
• August 03, 2021 04:33
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• 0 votes

1. Community
2. Non-Human
3. Error Creatting Dictionary for genome

Hello I have exactly the same problem with hg38 reference genome downloaded from google resources of broad institute. I would be thankful if you let us know whether you found the solution?    Best  

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• zdr j
• August 02, 2021 08:27
• 0 votes