jorgez
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Latest activity by jorgez-
jorgez commented,
Hello Genevieve, Thanks so much for the explanation. It's perfectly clear now. Best Jorge
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jorgez created a post,
MTLowHeteroplasmyFilterTool documentation
AnsweredHello, b) What does the --max-allowed-low-hets MTLowHeteroplasmyFilterTool parameter mean? the help argument says:Number of low het sites allowed to pass other filters before filtering out all low ...
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jorgez created a post,
identify heteroplasmic variants MTLowHeteroplasmyFilterTool
Hello, This is not an error but a How do I... question. How do I separate the variants coming from the major constituent mtDNA from the heteroplasmic variants? I have run the mitochondria-pipeline...
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jorgez created a post,
CombineVariants set attribute filters on all callers explicitly (not with filteredInAll)
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 3.7-0-gcfedb67 b) Exact command used: java -jar $EBROOTGATK/GenomeAnalysisTK.jar -T CombineVariants \-R hg38.fa \--vari...
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jorgez commented,
Hi, Not on vcf files produced by either Platypus or VarScan. Jorge
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jorgez commented,
Hi again, I did a bit of testing and confirmed that FixVcfHeader works on vcf files produced by GATK and SAMtools but it fails in vcf files produced by VarScan or Platypus. This is the behaviour I ...
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jorgez commented,
Hi, This is the log for IndexFeatureFile (A) and FixVcfHeader (B) A: IndexFeatureFile Using GATK jar /mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Core/gatk/4.1.7.0/gatk-package-4.1.7.0...
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jorgez commented,
Hi, Yes, the index was created successfully with IndexFeatureFile
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jorgez commented,
Hi, Both (A) the usual sort, bgzip and tabix sequence followed by FixVcfHeader or (B) or IndexFeatureFile followed by FixVcfHeader fails with the error 'A reference dictionary is required for cre...
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jorgez created a post,
FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly
Hello GATK team, I'm getting an error when using FixVcfHeader. The error complains about a reference dictionary which is required for creating Tribble indices on the fly. Could you please tell me h...