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• what the "cycle" mean in MeanQualityByCycle of picard
  Hi, I use picard tool "CollectBaseDistributionByCycle" to plot a figure "CollectBaseDistribution...
• What is the difference between picard and picard-tools ?
  Hey, everyone. Does anyone know the difference between picard and picard-tools ? I think we use ...
• SAM flags meaning
  Hi all, I'm struggling with finding explanations to the SAM flags presented on my sam file. to c...
• Should quality scores be considered when discriminating between optical and library duplicates?
  Picard's MarkDuplicates tool is very useful. As far as I know it's the standard for identifying d...
• Is it okay to realign and subsequently process fastq files that were converted from processed BAM files?
  I have been given BAM files from a collaborator that have already gone through processing, but I ...
• Picard tools duplicate removal
  Hi, I want to use PICARD tools markduplicates option, but after reading the manual I am still not...
• picard FastqToSam is giving me "File not found"
  **when i run the following:** >~ $picard FastqToSam \ >F1=usr/local/Cellar/picard-tools/...
• CheckIlluminaDirectory exception: TileMetricsOutReader expects the version number to be 2. Actual Version in Header( 3)
  I'm trying to extract some BCL files generated by a NovaSeq run. When I run CheckIlluminaDirector...
• Picard MarkDuplicates.jar error
  Hi All Anybody know why am getting this error. I get it with version 1.92 and 1.77. $ /usr...
• Definition of PCR duplicates based on alignment coordinates
  Dear all, I have to identify PCR duplicates by myself and would like to understand how tools lik...
• BWA MEM alignment output of splited fastq files differ from the original(unsplit) fastq file
  Hi, I want to do alignment of paired end fastQ files (R1 and R2) for which I am using BWA MEM to...
• modification of WGS data with Picard
  The latest test result shows that Picard can handle our whole individual WGS bam file. Because GA...
• Picard MarkDuplicates error: Value was put into PairInfoMap more than once
  Hi, I saw this error encountered by a few other users and I tried all that was suggested but not...
• Difference between marking duplicates and filtering BAM on phred score
  Hey! I am working with whole genome sequencing data of bacterial samples and have done an Illumi...
• how to fix INVALID_FLAG_MATE_UNMAPPED sam flag
  Hi All, First time posting to biostars, so please forgive any formatting errors. Please let me ...
• QC for custom Ampliseq panels
  What tool is best to use get get QC metrics for ion data from custom ampliseq panels? I've seen t...
• What means "high quality" reference genome
  Hello, I'm new to Bioinformatics, just starting my second year, and there is a question I can't ...
• Picard MergeSam error : Cannot use index file with textual SAM file
  I tried to run a simple mergesam using picard on two bam files using the following command j...
• What does Picard tools cleansam and fixemate exactly do and what are the equivalents in samtools ?
  Hi, I'm wondering what do Picard Tools "cleansam" and "fixemate" exactly do to the data and what...