![]() ![]() The name includes the individual sample ID, where the sequence is mapped to, if the file has only contains mapping to a particular chromosome that is what the name contains otherwise, mapped means the whole genome mapping and unmapped means the reads which failed to map to the reference (pairs where one mate mapped and the other didn’t stay in the mapped file), the sequencing platform, the ethnicity of the sample using our three letter population code, the sequencing strategy. The bai index and bas statistics files are also named in the same way. There is a github page where the format of CRAM file is discussed and help can be found.ĬRAM files can be read using many Picard tools and work is being done to ensure samtools can also read the file format natively. The CRAM files the 1000 Genomes project distributes are lossy cram files which reduce the base quality scores using the Illumina 8-bin compression scheme as described in the lossy compression section on the cram usage page The CRAM file format was designed by the EBI to reduce the disk footprint of alignment data in these days of ever-increasing data volumes. This compression is driven by the reference the sequence data is aligned to. BAM is a standard alignment format which was defined by the 1000 Genomes consortium and has since seen wide community adoption, whereas CRAM is a compressed version of this. All our alignment files are in BAM or CRAM format. ![]()
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