Our filename conventions depend on the data format being named. This is described in more detail below.
Our sequence files are distributed in gzipped fastq format
Our files are named with the SRA run accession E?SRR000000.filt.fastq.gz. All the reads in the file also hold this name. The files with _1 and _2 in their names are associated with paired end sequencing runs. If there is also a file with no number it is name this represents the fragments where the other end failed qc. The .filt in the name represents the data in the file has been filtered after retrieval from the archive. This filtering process is described in a README.
Our variant files are distributed in vcf format, a format initially designed for the 1000 Genomes Project which has seen wider community adoption.
The majority of our vcf files are named in the form:
ALL.chrN|wgs|wex.2of4intersection.20100804.snps|indels|sv.genotypes.analysis_group.vcf.gz
This name starts with the population that the variants were discovered in, if ALL is specifed it means all the individuals available at that date were used. Then the region covered by the call set, this can be a chromosome, wgs (which means the file contains at least all the autosomes) or wex (this represents the whole exome) and a description of how the call set was produced or who produced it, the date matches the sequence and alignment freezes used to generate the variant call set. Next a field which describes what type of variant the file contains, then the analysis group used to generate the variant calls, this should be low coverage, exome or integrated and finally we have either sites or genotypes. A sites file just contains the first eight columns of the vcf format and the genotypes files contain individual genotype data as well.
Release directories should also contain panel files which also describe what individuals the variants have genotypes for and what populations those individuals are from.