CRAM files can be combined in a single one where all queries are aligned to the target, almost like in a multiple-sequence alignment.
Key points to remember to avoid temporary folder paths in the samtools header.
- create the samtools dictionary with a relative path to the genome file.
- make sure
samtools/sort is not allowed to call the EBI.
- remove
--reference from samtools/merge or find a better solution.
CRAM files can be combined in a single one where all queries are aligned to the target, almost like in a multiple-sequence alignment.
Key points to remember to avoid temporary folder paths in the samtools header.
samtools/sortis not allowed to call the EBI.--referencefromsamtools/mergeor find a better solution.