Data Formats

This page describes file formats used in Chromoscope. To find a list of required and optional files, please refer to the Data Configuration section.

Structural Variants (BEDPE)

The structural variants are stored in a headed BEDPE file. The order of the columns does not need to be in the exact same order. This is a The following columns are used in the browser:

Property	Type	Note
chrom1	string	Required. The name of the chromosome of the first break point (BP).
start1	number	Required. The starting position of the first BP.
end1	number	Required. The end position of the first BP.
chrom2	string	Required. The name of the chromosome of the second BP.
start2	number	Required. The starting position of the second BP.
end2	number	Required. The end position of the second BP.
sv_id	string	Required. The name of the SV.
pe_support	string	Optional. The number of events that support SV shown in tooltips.
strand1	string	Required. The strand for the first BP. Either '+' or '-'.
strand2	string	Required. The strand for the second BP. Either '+' or '-'.

Example file:

https://somatic-browser-test.s3.amazonaws.com/SVTYPE_SV_test_tumor_normal_with_panel.bedpe

SV Type Mapping Table

In Chromosope, strands are mapped with the following types of SVs.

Inter-chromosomal SV types	strand1	strand2
Deletion	+	-
Inversion (head-to-head)	+	+
Inversion (tail-to-tail)	-	-
Duplication	-	+

CNV (TSV)

The CNV is stored in a headed tab-delimited file that is visualized as three tracks: CNV, Gain, and LOH. The order of the columns does not need to be in the exact same order.

Property	Type	Note
chromosome	string	Required. The name of the chromosome.
start	number	Required. The starting position.
end	number	Required. The end position.
total_cn	string	Required. The total number of copies.
major_cn	number	Required. The major allele counts.
minor_cn	number	Required. The minor allele counts.

Example file:

https://s3.amazonaws.com/gosling-lang.org/data/SV/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.consensus.20170119.somatic.cna.annotated.txt

Drivers (TSV or JSON)

The drivers are stored in a headed tab-delimited file. When this file is present, the browser will show drivers that are included in the file only.

The order of the columns does not need to be in the exact same order.

Property	Type	Note
chr	string	Required. The name of the chromosome. The names should contain chr prefix, such as chr2 and chrX.
pos	number	Required. The position of the driver.
gene	string	Required. The name of the driver.
ref	string	Optional. Information only shown on a tooltip.
alt	string	Optional. Information only shown on a tooltip.
category	string	Optional. Information only shown on a tooltip.
top_category	string	Optional. Information only shown on a tooltip.
transcript_consequence	string	Optional. Information only shown on a tooltip.
protein_mutation	string	Optional. Information only shown on a tooltip.
allele_fraction	string	Optional. Information only shown on a tooltip.
mutation_type	string	Optional. Information only shown on a tooltip.
biallelic	string	Required. Either Yes or No. Whether the mutation occurs on both alleles of a single gene.

An annotation representing a biallelic mutation.

Based on the biallelic value, the browser shows annotations near the gene name:

• “⊙” for biallelic when the biallelic column is "yes"
• “.” for not biallelic (i.e., mono-allelic) when "no"
• no symbol when undefined

Example file:

https://gist.githubusercontent.com/sehilyi/350b9e633c52ad97df00a0fc13a8839a/raw/c47b9ba33f1c9e187c69d1dadd01838db44d3b29/driver.txt

VCF & TBI

For point mutations and indels, we use standard VCF files along with tabix files. To generate the tabix file, you can run the following command:

tabix myfile.sorted.vcf.gz

Refer to the documentation of Samtools for details (https://www.htslib.org/doc/tabix.html).

caution

The VCF files should be sorted and indexed to be able to make Chromoscope to properly show genomics features.

BAM & BAI

For read alignments, we use standard BAM files along with BAI files. To generate the index file, you can run the following command:

samtools index myfile.sorted.bam.gz myfile.sorted.bam.bai

Refer to the documentation of Samtools for details (https://www.htslib.org/doc/samtools-index.html).

caution

The BAM files should be sorted and indexed to be able to make Chromoscope to properly show genomics features.