Using samtools faidx with a large list of genomic loci

Question

[jsandler]

I'm using the faidx command with samtools to generate a fasta file with the sequences of various lists of genomic loci I am interested in. The lists of genomic loci contain ~100-1000 unique positions. I would like to include the file with the list of loci in the faidx command, but I am unable to get samtools to read this file. Instead, I am currently pasting in this list from the output of a sql query. Is there a file format that samtools can read that will save me the pain of cut and paste? Here is my command:

samtools faidx /<path to genome>/genome.fa loci_list.csv output.fa

The error returned is:

[W::fai_get_val] Reference loci_list.csv not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in loci_list

Thanks

Answer 1

[liorglic]

To do what you want, you need to run:

samtools faidx /<path to genome>/genome.fa -r loci_list > output.fa

and your loci_list should contain lines with the format: chr:start-end, not csv lines.
Alternatively, use bedtools getfasta as described here.