I am trying to retreive some genic regions from a .cram file, i know the workflow starting with .bam files, so i want to convert some whole low coverage genomes from cram to bam
I have been reading the manual and some how-to blogs, but i haven't come with a correct syntax to make the tool run and make the bams i need.
I know the syntax must have the reference genome in order to make the cram file readable, so i tried the next syntax:
samtools view -b <file.cram> <refgenome.fa> -o <file.bam>
it outputs the next error flag:
[main_samview] region "refgenome.fa" specifies an unknown reference name. Continue anyway.
and it does not build a usable .bam file, the flag is really straightforward, but i am sure that the reference genome i am using is correct, i think it is something about the syntax, i am using the -b flag at the beginning given the fact that i want an output file in bam format.
Any suggestions?, any help would be much appreciated!