How can I subset a reference based on only the first chromosome?
It sounds like you want samtools faidx foo.fa followed by samtools faidx foo.fa chr1 &gt; your_subset_file.fa (or whatever the first chromosome is). The output file is then a regular fasta file subset as you like. You can get any chromosome you want with that. In fact, you can also do regions (e.g., chr1:100-1000, though note that the sequence name in the resulting fasta output will be chr1:100-1000, which may break some downstream tools).