Illumina Pipeline version 1.3 Sequencing Support

Illumina Sequencing Support

IGV includes limited support for viewing alignments in the "sorted.txt" format from the Illumina Pipeline version 1.3, with the following restrictions.

  • The contig fields (columns 12 and 19) are not supported
  • The Match chromosome field (column 11) must either be the name of a chromosome in an IGV genome, or an entry in the seqname to chromosome mapping file defined below.

Mapping File: To view alignments from a sorted.txt file in which the chromosome names are not chromosome names in IGV, a mapping file must be provided. This is a 2-column tab-delimited file with chromosome names from the sorted.txt file in column 1, and corresponding IGV chromosome names in column 2. The file must be named "sequence.map" and placed in a specific directory, which is platform dependent:

Windows: <user home>/igv/sam
Linux: <user home>/igv/sam
Mac: <user home>/.igv/sam

On Windows computers the user home directory is normally found at:

C:/Documents and Settings/<user name>