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Using samtools faidx with a large list of genomic loci

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

samtools faidx alignment
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updated by Ram Ram • written by jsandler • jsandler

1 answer

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.

• 0 views • link
written by liorglic liorglic

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