Software
- Should I use Long Ranger, Supernova, or other tools to analyze 10x linked reads?
- 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?