Data Formats
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 |
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