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Software

  • Why does the longranger basic pipeline only output one FASTQ file when I gave it paired-end data?
  • Why do I see 0|0 genotypes in my Long Ranger output?
  • Why is my molecule size less than what I expected for my Chromium Genome library?
  • How many barcodes does Long Ranger need to call a structural variant?
  • What is the resolution (size of chromosomal rearrangement) that Long Ranger can detect with linked-read data? 
  • Why do some of the processed reads from the Long Ranger Basic pipeline not have barcodes associated with them?
  • Is it important to use the hs38d1 decoy in Long Ranger WGS?
  • What is the difference between a phase set in the Long Ranger VCF and a phase block in the Loupe Browser?
  • What is the HAPLOCALLED Info field?
  • There are variants between phase blocks in Long Ranger. Why were they not joined?
  • Can somatic mutations or low frequency variants be detected by Long Ranger?
  • Are linked reads helpful for targeted re-sequencing applications?
  • How can I identify PCR duplicates from Long Ranger output?
  • What is phasing quality (PQ) and what does it mean?
  • Why are some MI tags missing from the Long Ranger BAM file?
  • Why don't my reads have an HP tag in the Long Ranger BAM file?
  • Where can I find the Agilent Target BED files?
  • What are the Long Ranger QC metrics and thresholds?
  • Why are variants in my VCF file not displayed in the Loupe Genome Haplotype View?
  • How is the PCR duplication rate calculated in Long Ranger?
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