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10x Genomics
GemCode Genome & Exome

Reference Support

Long Ranger algorithms are tuned and optimized for human haplotype phasing and structural variant calling, and 10x Genomics provides pre-built hg19 and b37-style reference packages for use with the pipeline. The pre-built references have the following characteristics:

Use of the pre-built references is strongly recommended unless you have specific requirements that match one of the compatible use cases below:

Compatible Use Cases

Long Ranger supports the use of customer-generated references for the following scenarios:

Not Compatible

The following scenarios are not currently supported by Long Ranger:

Making a Reference Package

There are 3 steps to construct a Long Ranger-compatible reference. You must have version 1.1.1 or later of both Long Ranger and Loupe.

1. Index your FASTA

To create a reference, run the longranger mkref command on your FASTA file. The contigs in your FASTA must meet the compatibility requirements above.

$ longranger mkref hsapiens-asm19.fasta
... indexing may take over an hour ...
$ ls refdata-hsapiens-asm19
fasta/  genes/  genome  regions/  snps/

This utility copies your FASTA, indexes it in several formats, and outputs a folder named refdata-<fasta_name>.

2. SV Calling Blacklist

At this point, the reference folder created by longranger mkref is usable by Long Ranger, but it is strongly recommended that you also include a region blacklist for structural variant calling.

 The blacklist is used by the SV algorithm to reduce false positives due to gaps in the reference, known or putative assembly issues such as unplaced contigs, and highly polymorphic regions.

For hg19 references, we provide pre-built blacklist files that you can simply copy into your reference. Follow the instructions below, depending on the naming convention of your reference:

hg19 Convention ("chr1")

$ cd refdata-hsapiens-asm19
$ cd regions
$ wget
$ wget

b37 Convention ("1")

$ cd refdata-hsapiens-asm19
$ cd regions
$ wget
$ wget

For all other references, follow these instructions to create custom blacklist files.

3. Genes/Exons File for Loupe

To enable the display of the genes and exons tracks in the Loupe genome browser, download our genes and exons file into your reference. This file will work regardless of the naming convention of your reference.

$ cd refdata-hsapiens-asm19
$ cd genes
$ wget

This step is optional, but if you omit this file, you will not be able to search by gene name in Loupe, or see the genes and exons tracks in the Loupe Haplotype view. Please note that modifying this file is not supported.

4. Confirm Contents

If you have followed the steps above correctly, your reference folder should now contain the following files:

$ tree refdata-hsapiens-asm19
├── fasta
│   ├── genome.fa
│   ├── genome.fa.amb
│   ├── genome.fa.ann
│   ├── genome.fa.bwt
│   ├── genome.fa.fai
│   ├── genome.fa.flat
│   ├── genome.fa.gdx
│   ├── genome.fa.pac
│   └──
├── genes
│   └── loupe_genes_exons.tsv
├── genome
├── regions
│   ├── segdups.bedpe
│   └── sv_blacklist.bed
└── snps
4 directories, 13 files

Running Long Ranger

To run Long Ranger with your new reference, set the --reference argument of longranger run to your new reference:

$ longranger run --reference=/path/to/refdata-hsapiens-asm19 ...