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2. General Discussion
3. MGI DNBSEQ-T7 DNA Sequencer (Nebula) ….Is it Compatible with GATK Best Practice Pipeline?

Completely compatible. Use ILLUMINA as platform tag in sam file. Picard or GATK does not accept MGI as platform name. General base quality and call metrics are very compatible with earlier ILLUMINA...

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• SkyWarrior
• April 02, 2021 16:18
• 3 votes

1. Community
2. Other
3. Problem Installing GATK python environment - SOLUTION POSTED!

Looks like I found the solution to this problem but this may only be a temporary solution so devs please check this requirement of gatk environment and merge a solution.  This gatk conda environmen...

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• SkyWarrior
• February 06, 2020 07:19
• 3 votes

1. Community
2. Germline
3. GermlineCNVCaller - I don't have a cohort, use public data?

Hi paalmbj Short answer: Don't even bother.  Long and convoluted answer: There may be a duct tape solution you may try. Check 1000G whole exome files however the capture kit compatibility will be a...

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• SkyWarrior
• July 24, 2023 13:56
• Edited
• 2 votes

1. Community
2. General Discussion
3. Haplotypes of duplicated genes

Not with short read sequencing technologies. 3N does not always mean 3 different haplotypes BTW. 3 copies of the same haplotype or 2 copies of one haplotype and 1 copy of another haplotype can also...

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• SkyWarrior
• April 07, 2021 12:06
• 2 votes

1. Community
2. Germline
3. The optimization step for ELBO update returned a NaN

3000 genomes seems to be too much. How much memory do you have available for this analysis? Also have you tried the docker version of gatk especially 4.1.7.0 (latest one compatible with skylake and...

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• SkyWarrior
• February 16, 2021 13:02
• Edited
• 2 votes

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2. Other
3. Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH

You may want to use OpenJDK Hotspot instead of OpenJ9.  Can you check with AdoptOpenJDK?    

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• SkyWarrior
• March 02, 2020 11:06
• 2 votes

1. Community
2. Somatic
3. UnifiedGenotyper error on Solid data

This is a galaxy wrapper fault not GATK.

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• SkyWarrior
• February 21, 2020 05:56
• 2 votes

1. Community
2. Germline
3. GermlineCNVCaller - Cohort mode - samples size recommendation.

Hi Ram All my samples are in-house clinical samples validated using other orthogonal methods. I routinely check the results of all the cohort samples once new members are added and I observe the ch...

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• SkyWarrior
• March 26, 2024 03:11
• 1 vote

1. Community
2. New User Advice
3. Read Groups - which platform (PL) to specify for Element Biosciences reads?

Hi Salvatore Loguercio Latest SAM Spec indicates the below comment PL | Platform/technology used to produce the reads. Valid values: CAPILLARY, DNBSEQ (MGI/BGI),ELEMENT, HELICOS, ILLUMINA, IONTORR...

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• SkyWarrior
• February 15, 2024 08:00
• 1 vote

1. Community
2. General Discussion
3. GetPileupSummaries Empty File Output

Hi William Miklavcic Looks like your archnemesis lies with your heap size. Exception in thread "main" java.lang.OutOfMemoryError: Java heap space It is better if you can set java options with highe...

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• SkyWarrior
• January 18, 2024 12:08
• 1 vote