Questions about transfering wgs file to reference genome file

Question

[me]

Hi, I have a task to transfer cram file to fa file. For example, I have a cram file named as chr_123.cram.

I intend to use samtools to transfer this file to fa file, with reference genome hg38.fa. The out file should be chr_123.fa.

My chr_123.fa should contain chr information, for example:

>chr1
........................

But my current method (samtools) only uses my fa file, and my file does not contain chr information. It contains information like:

>H25LYCCXX150109:3:2222:11535:23653/1
GGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGATATCGGAAGAGCACACGTCTGAACTCCGGTTAGGTATGCGTATAGCGTATGGGGTCTTGTGATTGAAAAAGTAAG

Thanks.

[ATpoint]

What does "transfer" mean? Is this aligned data and you want a consensus sequence? What exactly do you need.

[me]

Hi, thanks for your reply. I think it may not be teh consensus sequence. I intend to have an individual genome file, that is, each chr contains individual sequence information.

[ATpoint]

I intend to have an individual genome file, that is, each chr contains individual sequence information.

That is what a consensus sequence is. See https://www.htslib.org/doc/samtools-consensus.html

[me]

Thanks a lot. That seem the exact thing I am looking for!