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
GENE	quant.genes.sf, quant.genes.sf.gs	No
GFF	.gff	No
GIF	.gif, .GIF	Yes
GTF	.gtf	No
GVCF	.gvcf, .gvcf.gz, .hard-filtered.gvcf, hard-filtered.gvcf.gz	No
GZ	.gz	No
HTML	.htm, .html	Yes
INSER	.inser	No
JPG	.jpg, .JPG, .jpeg, .JPEG	Yes
JSON	.json, .hard-filtered.json, .hard-filtered.json.gz, .sv.json, .sv.json.gz	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, .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
TRANSCRIPT	.quant.sf, .quant.sf.gz	No
TSV	.tsv, .maf	Yes
TXT	.txt, .TXT, .out, .err, .log, .Rlog	Yes
UNKNOWN		No
VCF	.vcf.gz, .vcf, .hard-filtered.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