Convert a cram file to fasta

Question

[Samanta]

How can I go from a cram file to a fasta without having to convert to a .bam, index and map?

At the moment I'm trying to pass bam, but I'm not succeeding either

I already tried with this line

samtools view -b -T /media/SSD1/reference.fasta -o 15132.bam 15132_657.cram

but it throws me this error

[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/17d0aca68c27ef37c9f0ebbd12de292b": Protocol not supported
[E::cram_get_ref] Failed to populate reference for id 1
[E::cram_decode_slice] Unable to fetch reference #1 206..211482
[E::cram_next_slice] Failure to decode slice
[main_samview] truncated file.

[GenoMax]

Something like this may be simpler:

samtools view -b -T /media/SSD1/reference.fasta 15132_657.cram | samtools sort -n - | samtools fasta ...option

That said it appears that you may be using incorrect reference.See: Failed to populate reference for id 1?

You may be able to simply use

$ samtools fasta
Usage: samtools fasta [options...] <in.bam>

Description:
Converts a SAM, BAM or **CRAM** to FASTA format.

[cmdcolin]

what is your ultimate goal in "converting CRAM to FASTA"

[Samanta]

To do my selection and linkage disequilibrium assays

[cmdcolin]

You will likely not be closer to your goal by converting CRAM to FASTA. Instead you likely want to do variant calling on your CRAM file(s) to generate a VCF, and do population analysis and things on that. see linkage disequilibrium analysis for an example of linkage disequilibrium analysis on a VCF. It is often important to be clear about what your end goal is when asking a question because "converting CRAM to FASTA" is sort of a non-sense operation (the answer given above converts each individual read to a line in the FASTA, which is rarely what you want), it's much more common to analyze your variants in VCF/PLINK style workflows. see also https://pixy.readthedocs.io/en/latest/