User: pjb39

gravatar for pjb39
pjb3960
Reputation:
60
Status:
New User
Location:
USA/Ithaca,NY/USDA-ARS
Last seen:
2 weeks, 3 days ago
Joined:
9 months, 3 weeks ago
Email:
p****@cornell.edu

Posts by pjb39

<prev • 14 results • page 1 of 2 • next >
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Answer: A: PHG ImputePipelinePlugin with VCF as input is incomplete?
... The developer who wrote the Impute pipeline thought that the SNPToReadMappingPlugin would write directly to the database but it does not. Instead, it writes the read mappings to files as you noticed. We discovered that a short time ago. There is code in testing to allow SNPToReadMappingPlugin to wri ...
written 26 days ago by pjb3960
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Comment: C: GetHapIdsForTaxonPlugin method question
... If the only change you made was changing pathHaplotypeMethod from CONSENSUS_mxDiv0.0001 to CONSENSUS_mxDiv0.0001,refRegionGroup that suggests that refRegionGroup is not a valid referenceRange group name. If that does not make sense, you can send me the log file. Something else in the log may indicat ...
written 3 months ago by pjb3960
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Comment: C: GetHapIdsForTaxonPlugin method question
... The following command should work: sudo docker run --name hapPaths_assemblies --rm \ -v /home/kathrynmichel/KaepplerDeLeon-T330-Mount/Assemblies/PHG/Nov2020_B73v5/:/phg/ \ -t maizegenetics/phg:latest \ /tassel-5-standalone/run_pipeline.pl -debug -Xmx100G -configParameters /ph ...
written 3 months ago by pjb3960
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Answer: A: GetHapIdsForTaxonPlugin method question
... GetHapIdsForTaxonPlugin should have returned some Haplotype ids as the above answer suggests. I do not know why that did not work. If what you want is a VCF rather than haplotype id lists, then you need to use PathsToVCF. To export a VCF for assembly (or WGS) haplotypes, you have to build a Haplotyp ...
written 3 months ago by pjb3960
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Answer: A: Impute variants from fastq files - homozygous error
... One possible cause is that the number of haplotypes for one or more reference ranges is greater than 127. If that is the case, then using consensus haplotypes should reduce the number below that. To make sure it does, you can add the parameter maxClusters to the config file used to create consensus ...
written 3 months ago by pjb3960
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Answer: A: PHG v0.0.23 (latest) LoadHaplotypesFromGVCFPlugin fails, but v0.0.22 with same s
... Looks like the first answer missed the second question at the bottom. The new code and bug affect loading haplotypes to the PHG db but do not affect the imputation pipeline. 0.0.23 does contain important improvements to the DiploidPathPlugin. So, you can use 0.0.23 for imputation but not for loading ...
written 4 months ago by pjb3960
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Comment: C: findPath using fastqs in sub-directories
... I have been doing some more testing. It turns out there is a bug after the recursive search. The code finds the filename in the right place then later looks for it in fastqDir because the person doing the downstream coding did not realize that the search was recursive. So, for now the fastq files al ...
written 4 months ago by pjb3960
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Comment: C: ImputePipelinePlugin diploidPath error (without error message), possible bug?
... The new build of the PHG docker contains a fix for this bug. ...
written 4 months ago by pjb3960
0
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Comment: C: findPath using fastqs in sub-directories
... What is the correct location of 11367.8.203207.ATGCACG-TCGTGCA.r1_cutadapt.fq and what the value of fastqDir? ...
written 4 months ago by pjb3960
0
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Comment: C: findPath using fastqs in sub-directories
... I answered too quickly. I reviewed the PHG code and found that it is already doing a recursive search. You should be able to specify the top level directory as the fastqDir for path finding and as long as the key files are in that directory or a subdirectory they should be found. You are correct tha ...
written 4 months ago by pjb3960

Latest awards to pjb39

Scholar 26 days ago, created an answer that has been accepted. For A: ImputePipelinePlugin diploidPath error (without error message), possible bug?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: ImputePipelinePlugin diploidPath error (without error message), possible bug?
Scholar 4 months ago, created an answer that has been accepted. For A: ImputePipelinePlugin diploidPath error (without error message), possible bug?

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