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TimestampWhat is the MIME type that you wish to add?What is the filename pattern?Add a description for your new MIME typeWhat known workflows use this column type?
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*.txt text/plain Plain text file (with Unix/Linux line breaks)
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11/12/2014 17:34:25application/tbi*.tbiTabix index FilesSampleFingerprinting, MutectStrelka, Bartlett, StructuralVariation, VariantAnnotation
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8/16/2017 10:20:01application/txt-gz*.txt.gz, *.cov.gzcompressed text filesBismark workflow
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*.json text/json JSON formatted text file
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*.gff text/gff3 A GFF variant file, see
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*.gff text/gff3-solid A GFF variant file, see , this is the specific GFF format from Life's SOLiD software suite as recognized by the Annovar conversion tool.
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*.annovar.consequence text/annovar-consequence Annovar coding consequence file
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*.annovar.consequence text/annovar-consequence-exonic-variant-fxn Annovar coding consequence file
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*.annovar.consequence text/annovar-consequence-variant-fxn Annovar coding consequence file
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*.annovar.dbsnp text/annovar-dbsnp Annovar dbsnp overlaps file
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*.annovar.dbsnp text/annovar-dbsnp-filtered Annovar dbsnp overlaps file
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*.annovar.dbsnp text/annovar-dbsnp-dropped Annovar dbsnp overlaps file
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*.annovar.omim text/annovar-omim Annovar omim overlaps file
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*.annovar.tags text/annovar-tags Annovar annotations in tag format
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*.sai application/bwa-sai Intermediate file from the "aln" step of BWA.
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*.bam application/bam BAM alignemt file
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*.sam text/sam SAM alignemt file
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*.bai application/bam-index BAM index file
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*.pileup text/pileup The output format pileup from the SamTools variant caller
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*.pileup.gz application/pileup-gzip The output format pileup from the SamTools variant caller compressed with gzip
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*.pileup text/pileup-consensus The same output format pileup from the SamTools variant caller but with the addition of the SOAPsnp consensus sequence
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*.vcf text/vcf-4 The Variant Call Format version 4, either 4 or 4.1 (see ) for encoding SNPs and other genomic features.
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*.vcf.gz application/vcf-4-gzip The Variant Call Format version 4, either 4 or 4.1 (see ) for encoding SNPs and other genomic features. This meta type is for a standard vcf file that has been gzipped.
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*.srf application/srf SRF formated sequence file from Short Read Archive
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*.kv text/key-value any key-value file, has two columns sep by tab, key tab value, useful for QC reports
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*.report.zip application/zip-report-bundle A zip of a directory that contains an index.html in its root and 0 or more other files. This is de-compressed on the fly by the Seqware Portal and displayed to the user. We use this to store multi-file, rich, HTML reports that contain many individual png files.
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*.tar.gz, *.tgz application/tar-gzip A bundled set of compressed files
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*.h-mito.txt text/h-mito sample mitochondrial haplogroup prediction
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*.transcript.quantification.txt text/transcript-quant read count, coverage, & RPKM at transcript level
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*.gene.quantification.txt text/gene-quant read count, coverage, & RPKM at gene level
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*.exon.quantification.txt text/exon-quant base count, coverage, & RPKM at exon level
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*.spljxn.quantification.txt text/junction-quant counts at splice junction level
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*.bigWig application/bigWig UCSC bigWig format
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*.maf text/maf Multiple alignment format
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*.bed text/bed BED genome browser track annotation file
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*.bigWig application/bigWig UCSC bigWig format
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*.fa chemical/seq-na-fasta Sequences in fasta format
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*.fq or *.fastq chemical/seq-na-fastq Sequences in fastq format
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*.fq.gz or *.fastq.gz chemical/seq-na-fastq-gzip Sequences in fastq format compressed with gzip
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*.csfasta chemical/seq-na-csfasta Sequences in csfasta format
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*.trmap text/transcript-mapping Flat file of transcript/genome pairwise alignment coordinates & transcript/gene relationship
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*.gtf text/gtf Sequence entries in GTF format
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*.composite.txt text/composite-reference Flat file of composite transcript and pairwise alignment coordinates
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*.exon.txt text/exon-reference Flat file of composite exons
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*.spljxn.txt text/junction-reference Flat file of known splice junctions
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*.fa.amb text/BWA-index-amb BWA index file (1 of 8 generated by BWA index -a bwtsw)
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*.fa.ann text/BWA-index-ann BWA index file (1 of 8 generated by BWA index -a bwtsw)
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*.fa.bwt text/BWA-index-bwt BWA index file (1 of 8 generated by BWA index -a bwtsw)
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*.fa.pac text/BWA-index-pac BWA index file (1 of 8 generated by BWA index -a bwtsw)
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*.fa.rbwt text/BWA-index-rbwt BWA index file (1 of 8 generated by BWA index -a bwtsw)
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*.fa.rpac text/BWA-index-rpac BWA index file (1 of 8 generated by BWA index -a bwtsw)
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*.fa.rsa text/BWA-index-rsa BWA index file (1 of 8 generated by BWA index -a bwtsw)
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*.fa.sa text/BWA-index-sa BWA index file (1 of 8 generated by BWA index -a bwtsw)
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*.* text/MapSplice-output-* One of many different output files generated by MapSplice.
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*.deletion, *.divergent, *.inversion, or *.translocation text/GASV-input GASV input file format (produced by BAM_preprocessor.pl)
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*.deletion.clusters, *.divergent.clusters, *.inversion.clusters, or *.translocation.clusters text/GASV-cluster-file GASV cluster files
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*.pdf application/pdf PDF files
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*.fpkm_tracking text/fpkm-tracking FPKM tracking files
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