10x Genomics
Genome & Exome

Long Ranger, printed on 12/21/2024

Release Notes for 2.1

Long Ranger 2.1.6

• Properly ignore SIGHUP when a pipeline is run using nohup.

Long Ranger 2.1.5

• Log only environment variables relevant for troubleshooting.

Long Ranger 2.1.4

wgs / targeted pipelines

• Add support for GATK 3.7.
• Add --downsample parameter to wgs and targeted pipeline to specify gigabases of sequencing data to used by pipeline.
• Fix extreme slow-down observed in DETECT_OVERLAPS and GET_READPAIR_EVIDENCE.
• Don't require Illumina-style FASTQ headers.
• Reduce memory consumption of PHASE_SNPINDELS. Improves run-time especially in local mode with < 6GB per core.
• Reduce size of chunks in PHASE_SNPINDELS when rate of heterozygosity is very high. Avoid extremely long-running chunks.
• Various speed and robustness improvements when using an assembly as the reference.
• Handle 0-length and very short reads gracefully (issue observed with heavily trimmed NextSeq reads).
• Add toolkit for fetching all reads from a given set of barcodes (contact [email protected] for more details).

mkfastq

• Add NovaSeq support to mkfastq.
• Now compatible with bcl2fastq 2.19.
• Add --id parameter to set the output folder name to something other than the flowcell.
• Detects case when the bcl2fastq process is killed mid-demultiplex, and stops the pipeline.
• More efficiently estimates the number of GEMs for runs with many 10x samples.
• Fixes a bug demultiplexing a samplesheet with a mix of 10x and non-10x samples with an underlying bcl2fastq version of 2.18 or higher.

Job Scheduling

• Fix several cases where, after mrp (which is invoked by longranger) gets killed, it was not able to restart correctly.
• On SGE clusters, longranger/mrp now periodically runs qstat to verify that the jobs it queued have not been killed or canceled.
• If the run fails, instead of just displaying a message pointing the user to the relevant _errors file, the contents of that file is printed.
• On automatic retry of failed stages, the reason for the original failure is logged.
• mrp is now more resilient against certain kinds of filesystem errors.
• In the event of certain types of filesystem problems (such as permissions errors or disk quota), mrp/longranger should now sometimes be able to provide more useful and immediate error messages.
• Additional information about the environment longranger runs in is now logged and included in mri.tgz.
• mrp now correctly handles the signals sent by SGE and LSF when a soft time limit is reached (e.g. for SGE, -l s_rt 23:00:00).
• Now supports --overrides method to dynamically change additional CPU and memory per stage.

Long Ranger 2.1.3

• Fixes issue preventing mkfastq from demultiplexing data from recent sequencer software versions.
• Fixes bug in calculating R1/R2 read-specific metrics.
• Updates BAM headers in ALIGN/BASIC to allow complete conversion from BAM to fastq.
• Fixes Lariat issue causing incorrect BAM sort order for some references.
• Skips ulimit preflight check on local machine when running in cluster mode.
• Fixes underflow issue in ANALYZE_SV_CALLS2.
• Improves VCF format correctness.

Long Ranger 2.1.2

• Add auto-retry mechanism when pipeline stages fail due to causes that appear to be transient.
• --maxjobs now defaults to 64 in local jobmode.
• --jobinterval now defaults to 100ms in local jobmode.
• Fix for rare race condition in some Python components.
• Add VCF header definition for HAPLOCALLED flag. VCF files should now validate in Picard.

Long Ranger 2.1.1

• Fixes issue preventing mkfastq from running bcl2fastq in certain circumstances.

Long Ranger 2.1.0

General

• Main pipeline now split into longranger wgs and longranger targeted (exome)
• Improved clarity and grouping of arguments in all --help output

New mkfastq Demultiplexing Pipeline

• Easier to integrate with existing bcl2fastq-based workflows
• Now the preferred demultiplexing method, demux still available but deprecated
• mkfastq is a thin wrapper around bcl2fastq with same basic interface
• Accepts Illumina Experiment Manager-compatible sample sheets with support for 10x sample index sets
• Produces FASTQ files and folders in the same structure as bcl2fastq
• Generates InterOp output for SAV
• Also generates 10x-specific run QC metrics in JSON format

Variant Calling Performance

• New haploid caller calls variants separately on each haplotype
• Haploid caller runs either Freebayes or GATK in haploid mode
• Calls are layered on top of existing calls generated in normal diploid mode
• Long Ranger GATK mode now requires GATK 3.3 or higher, excluding 3.6 (details). (Built-in FreeBayes mode still supported)

Mid-scale deletion calling

• New algorithms for calling deletions 50bp-30Kbp in WGS and Exome

Large-scale SV Calling Performance

• Improved algorithm performance in WGS and Exome
• Distinct parameter settings for germline and somatic samples
• More intuitive quality scores for SVs that reflect barcode support
• SVs now output in both VCF and BEDPE format
• SV phasing information is incorporated into the BEDPE/VCF output in both Exome and WGS samples

Sample and Genome Support

• Automatic sex detection
• More flexible custom reference support
• Pre-built GRCh38 reference package

File Format Improvements

• BAM and VCF index files now generated with same basename as main file
• Library identifier pass-through to BAM
• PC tag phasing confidence
• TR, TQ tags added to BAM to enable lossless BAM to FASTQ conversion

Martian Runtime

• Pipestance output files (outs/) are no longer symlinks
• Partial stage restart
• Add output filename override, supports two output files having same basename
• Add --onfinish handler support
• Add support for units of KB and B for memory reservation in cluster job templates
• Pipestances now generate a UUID in _uuid

Loupe 2.1.2

• Provides compatibility with macOS Sierra.

Loupe 2.1.1

• Corrects display of sample sex in Summary view.

Loupe 2.1.0

New Phase Block View

• Displays phase blocks on a whole genome level
• Select, view, and zoom into individual phase blocks

Redesigned Haplotype View

• Completely new design for display of variants
• Variant types now differentiated by color, shape and size
• Variants now individually visible and selectable at much greater zoom-out levels
• New UI behavior highlights matched alleles on each haplotype
• New filters for viewing/hiding homozygous and heterozyous variants only
• Adds support for phased 50bp-30Kbp deletions now called by Long Ranger

Usability Improvements

• Improved UI responsiveness, status, and progress throughout