Lucas Kopecky Bobadilla
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Activity overview
Latest activity by Lucas Kopecky Bobadilla-
Lucas Kopecky Bobadilla created a post,
SplitNCigarReads generating truncated bam files
a) GATK version used: v4.1.8.1 b) Exact command used: SplitNcigars Hello I am getting a truncated bam file after running SplitNCigarReads. If I run samtools quickcheck on it I'm getting this: FI...
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Lucas Kopecky Bobadilla commented,
I actually figure it out by running the R script alone. It seems that it is needed to transform the csv file strings to factor. By adding changing the line 16 from: data <- read.csv(args[1]) to d...
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Lucas Kopecky Bobadilla created a post,
AnalyzeCovariates
Hello I am using the current 4.17 GATK version and I am trying to run AnalyzeCovariates. I ran the baserecalibrator to get the table file to run AnalyzeCovariates but I am getting this following ...
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Lucas Kopecky Bobadilla created a post,
mergeBam picard issue
Hello, I'm having issues with the mergeBam function from Picard. I getting the following error: Exception in thread "main" java.lang.IllegalStateException: Aligned record iterator (A00419:256:HK...
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Lucas Kopecky Bobadilla created a post,
RNA-seq - VCF file BQSR non-model organism
Hello, I am currently working with a non-model plant RNA-seq dataset for variant discovery. I started to follow the pipeline in the GATK website, but I got stuck at the BQSR step. I have an asse...