Hello all,

Is there a possible way to index bam files for large chromosomes(like wheat) using Rsamtools? Like in case of samtools using linux, .CSI (coordinate sorted index) is possible whereby .bam files for large chromosomes can be indexed. However, the .CSI index generated using samtools (through linux) is not compatible with MEDIPS or QSEA packages which are used to calculate CpG densities for MeDIP-Seq data.

Regards,