The ICA environment currently supports the following formats for data files:
| Format | File Extension (if applicable) | Preview available |
|---|---|---|
ADAT
.adat
No
AMBIG
.ambig
No
AVRO
.avro, .AVRO
No
BAI
.bai
No
BAM
.bam
No
BCL
.bcl, .cbcl
No
BED
.bed
No
BedGraph
.BedGraph, .bedGraph
No
BGEN
.bgen
No
BIM
.bim
No
BMP
.bmp, .BMP
Yes
COV
.cov
No
CRAI
.crai
No
CRAM
.cram
No
CSV
.csv
Yes
CYTOBAND
.cyt, .CYT
No
DEL
.del
No
DICT
.dict
No
DOCKER
No
FAI
fai
No
FAM
.fam
No
FASTA
.fasta, .fa
No
FASTQ
.fastq, .fastq.gz, .fq, .fq.gz
No
FASTQC
.fastqc, .fastqc.gz
No
FLAGSTAT
.flagstat
No
GEM
.gem
No
GFF
.gff
No
GIF
.gif, .GIF
Yes
GTF
.gtf
No
GVCF
.gvcf, .gvcf.gz, hard-filtered.gvcf.gz
No
GZ
.gz
No
HTML
.htm, .html
Yes
INSER
.inser
No
JPG
.jpg, .JPG, .jpeg, .JPEG
Yes
JSON
.json
Yes
JSON_NEWLINE
.ndjson
No
KINSHIP
.kinship
No
LEN
.len
No
LOOM
.loom
No
ORA
.ora
No
MATRIX
.matrix
No
PARQUET
.parquet, .PARQUET
No
.pdf, .PDF
Yes
PGEN
.pgen
No
PNG
.png, .PNG
Yes
PSAM
.psam
No
PVAR
.pvar
No
RDATA
.Rdata, .RDATA, .RData, .rdata
No
SAM
.sam
No
SAMPLEMETADATA
No
SNP
.snp
No
SVG
.svg, .SVG
Yes
TAR
.tar.gz, .tar, .tgz, v8.tar, V8.TAR, v9.tar, V9.TAR
No
TBI
.tbi
No
TIFF
.tiff
Yes
TSV
.tsv, .maf
Yes
TXT
.txt, .TXT, .out, .err, .log, .Rlog
Yes
UNKNOWN
No
VCF
.vcf.gz, .vcf .hard-filtered.vcf.gz, .cnv.vcf.gz, .sv.vcf.gz, .repeats.vcf.gz
No
VCF.IDX
.vcf.idx
No
WSI
.wsi
No
XLSX
.xls, .xlsx
Yes
XML
.xml, .XML
Yes
YPILEUP
.ypileup
No
ZARR
.zarr
No
ZIP
.zip
No