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VQSR vs Hard Filtering
Hi, I’m analyzing >200 human exomes following GATK Best Practices. I’ve tried to read all the GATK documentation about this, but I’d like to ask you something just to be sure. I understand that it ...
cfDNA targeted sequencing - analysis pipeline
Hi there, I have human DNA samples isolated from tissue and from plasma, which were targeted sequenced on Ion Torrent. I've read some papers and blogs about the data analysis pipeline, but it looks...
genomicDBimport ERROR: java.lang.NumberFormatException: For input stringAnswered
Hi there, I had to redo the calling of two of my samples, and now I am trying to redo my genomic database in order to replace these two samples. My script:module load gatk/188.8.131.52 gatk --java-opti...
GenotypeGVCF by intervals
Hello, I have a batch with 219 samples /human exomes), on which I ran genomicsDBimport by chromosomes without a problem. I am now running GenotypeGVCF also by chromosomes; for chr 1-15, the jobs co...
Combine and Genotype GVCF - running timeAnswered
Hello. I am analysing 220 human exomes. I am running CombineGVCF, which is taking a lot of time. I know that it is slower than GenomicsDBImport, so I'm combining separately by chromosomes. Still, i...
AbstractAlignmentMerger Wrote 0 alignment records and 71729386 unmapped
Hi there, I am trying to align my fastq data (germline, whole exome sequencing, paired-end with illumina Novaseq). I already did the FastqToSam, MarkIlluminaAdapters and SamtoFastq, but I am having...