Commit e4b33dea authored by Mikaël Salson's avatar Mikaël Salson Slightly document BAM files

Fix #2553
parent c6fbe30a
......@@ -217,6 +217,10 @@ or =.fastq= file, possibly compressed with gzip (=.gz=).
This set of reads can reach several gigabytes and 2*10^9 reads. It is
never loaded entirely in the memory, but reads are processed one by
one by the Vidjil algorithm.
Vidjil can also process BAM files, but please note that:
1. The reads don't need to be aligned beforehand.
2. In case of paired-end sequencing, the reads must have already been merged
in the BAM file.
The =-h= and =-H= help options provide the list of parameters that can be
used. We detail here the options of the main =-c clones= command.
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