I am trying to use a tool called Telomerecat for estimating telomere length.
The tool takes BAM file as input.
I would like to use CRAM file as input instead of BAM files.
Anyone has tried it in the past using CRAM files? Because the bam files are ~ 100gb each. If I process 100-1000 storage is the issue.
I tried this command,
samtools view -T reference.fasta -b -h | Telomerecat bam2length - —output telomere_length.csv
This give me error.