convert CRAM file to SAM file

Question

I have a 50GB *.CRAM file and I need to convert it into *.SAM file My reference genome is hg38 and I got this CRAM from Nebula genomics How can I do it?

Answer 1

samtools view -T path/to/ref_genome -o out.sam in.cram

Be aware that this is going to be a gigantic files, hundreds of GBs, think about if this is really what you need or if downstream processing can use CRAM or BAM directly rather than SAM which is a plain uncompressed text file.