1. Community
2. General Discussion
3. GATK-SV QUAL values

Hi Matthew Hobbs, thanks for your question. I'm unsure about the QUAL mode at ~100, but I'd suggest looking at GQ instead. Typically we filter variants using GQ by converting genotypes with GQ belo...

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• Mark Walker
• March 04, 2024 22:25
• 0 votes

1. Community
2. Non-Human
3. PathSeqBuildReferenceTaxonomy is returning an error as `A USER ERROR has occurred: Bad input: Expected taxonomy ID to be an integer but found "4OWNbacteria|complete"`

Hi Abhilash Tripathi, I wasn't able to reproduce your error with RefSeq-release221.catalog.gz. Is it possible your file is corrupted? The md5sum I get is e600678fde0c8656012541890b2d8b31 if you wan...

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• Mark Walker
• February 14, 2024 21:22
• 0 votes

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2. Other
3. PathSeq freezing

Hi John Perkins, BWA will use off-heap memory to load the microbe index, so you want to make sure you have plenty of headroom for that. I'd suggest reducing the Java heap memory to the total memory...

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• Mark Walker
• November 17, 2023 17:02
• 0 votes

1. Community
2. Special GATK Use Cases
3. PathSeq: Should i build my Microbe DB from RNA (transcript) or DNA sequences when dealing with RNA-seq data?

Hi Renald James Legaspi, I agree, using a transcript reference may help with microbe detection sensitivity and specificity for RNAseq data and sounds appropriate for your case. For your host filter...

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• Mark Walker
• October 20, 2023 14:09
• 0 votes

1. Community
2. General Discussion
3. How to calculate the relative abundancy of microbes of a certain genus according to the output taxonomic file?

Hi Siyao Zhang, If I understand correctly, you are asking how to get the score normalized by all kingdoms and not just one. Since no other kingdoms are present, the reported "score_normalized" woul...

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• Mark Walker
• October 20, 2023 13:55
• 0 votes

1. Community
2. General Discussion
3. Individual bwa, dict files, and tax files for bacteria, fungi, and viruses.

Hi Caitlin Newman I don't believe we have a version of the microbe reference that's split up. The majority of the reference sequence has been bacteria. The full reference was created automatically ...

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• Mark Walker
• October 20, 2023 13:46
• 0 votes

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2. Non-Human
3. PathseqPipelineSpark stop with error message regarding com.esotericsoftware.kryo.KryoException: Buffer underflow.

Hi Shangru Li,  I'd recommend using the best practices host reference files, including the pre-built k-mers file. Note the host reference does not need to correspond the reference your data is alig...

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• Mark Walker
• September 15, 2023 13:54
• 0 votes

1. Community
2. General Discussion
3. cutting down on db or fa file based off of .txt results in pathseqspark

Hi caitlin newman, That information is contained in the refseq catalog, which can be found here: gs://gatk-best-practices/pathseq/resources/RefSeq-release91.catalog.gz The first column contains the...

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• Mark Walker
• August 30, 2023 19:11
• 1 vote

1. Community
2. Webinar Discussion: DRAGEN-GATK [Oct 2022]
3. Germline Copy Number Variant pipeline DRAGEN-GATK

Ok, WES contains many more sources of noise than WGS, so I would suggest adding more samples to your training set if possible.

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• Mark Walker
• July 26, 2023 15:21
• 1 vote

1. Community
2. Webinar Discussion: DRAGEN-GATK [Oct 2022]
3. Germline Copy Number Variant pipeline DRAGEN-GATK

Hi Joshua Ravi, The gCNV pipeline can be run from reads (bam or cram) aligned with either bwa or the DRAGEN pipeline aligner. There are only minor functional differences between these tools. 7 samp...

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• Mark Walker
• July 25, 2023 15:10
• 1 vote