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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. Germline
3. CombineGVCF on chr6，7，8，9，X hg38 running for ever~

Hi  Contents of the genomicsdb folder looks OK. Those commands also look fine. You may want to tweak the number of samples per batch if your problem still persists. But even if this does not solve ...

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• SkyWarrior
• February 19, 2024 18:47
• 0 votes

1. Community
2. Germline
3. CombineGVCF on chr6，7，8，9，X hg38 running for ever~

Hi again. Both tools will suffer from trying to load all samples all at once. GenomicsDBImport has a feature to load samples to genomics db in batches therefore tool will consume less memory and wi...

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• SkyWarrior
• February 19, 2024 13:50
• 0 votes

1. Community
2. Germline
3. CombineGVCF on chr6，7，8，9，X hg38 running for ever~

Hi XiuChao Wang Can you elaborate a little more on your compute environment?  Also CombineGVCFs tool is although useful combining too many samples is not a recommended way of operating joint genoty...

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• SkyWarrior
• February 19, 2024 10:40
• 0 votes

1. Community
2. Documentation Questions
3. VCF allelic depth (AD) supports the reference or alternate?

Hi Nikki Lukasko Can you provide us conflicting VCF entries from your results that could have caused this confusion? 

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• SkyWarrior
• February 16, 2024 22:03
• 0 votes

1. Community
2. Documentation Questions
3. VCF allelic depth (AD) supports the reference or alternate?

Oh I see. AD tuples or let's say arrays are designed to support the alelles in their given order. Allele number 0 is always the reference allele. Anything above index 0 is considered an alternate a...

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• SkyWarrior
• February 16, 2024 04:40
• 0 votes

1. Community
2. Documentation Questions
3. VCF allelic depth (AD) supports the reference or alternate?

Hi Nikki Lukasko The main identifier is in the GL/PL field where the likelihood of the called genotype is expressed in -10*log scale. Looking at your FORMAT field the likelihood of that site being ...

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• SkyWarrior
• February 16, 2024 00:33
• 0 votes

1. Community
2. Special GATK Use Cases
3. ASEReadCounter - What to use as the VCF variant reference

Hi Ferran Llobet Cabau You may check the latest documentation on the tool and the reference bioarxiv paper about this tool. Looks like the 3rd one is the choice for you.  https://gatk.broadinstitut...

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• SkyWarrior
• February 15, 2024 22:04
• 0 votes

1. Community
2. General Discussion
3. LeftAlignIndels Alignments added out of order... Offending records are at [chr7:55268881] and [chr7:55268881]

Hi James Covino I am not sure if you could solve your issue but let me ask. Have you observed any weird reads within bedtools intersect output via IGV or just samtools view command ? Would you be a...

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• SkyWarrior
• February 15, 2024 21:55
• Edited
• 0 votes

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