Index genome not working in Tracy

Question

[Joe]

I'm trying to follow the variant calling guide for Tracy.

https://www.gear-genomics.com/docs/tracy/cli/#variant-calling

I have a viral genome just as a fasta file, and when I try to call variants like this:

tracy decompose -v -a cmv -r CMVrefGenome.fasta -o oututfile inputfile.ab1

It tells me the genome needs to be shorter than 50kb, or indexed. I tried running this with a smaller fasta file only including the part I'm interested in, and this code worked. But when I tried to put the vcf files (converted from the bcf files) into IGV, they can't be read (I get the error ("filename.vcf null"). I don't understand why they can't be read. Therefore, I am trying this again but instead of cutting out a part of the genome, I want to use the exact same reference genome file in IGV, and maybe this will work. Therefore, I need to index the genome instead of cutting out just a piece. Tracy talks about genome indexing here:

https://www.gear-genomics.com/docs/tracy/cli/#trace-alignment

But when I try this with my fasta file, it says "Done" but then no file appears in the folder. On this page they say an fm9 file should appear with this command (https://github.com/gear-genomics/tracy/issues/4):

tracy index -o CMVrefGenome.fasta.fm9 CMVrefGenome.fasta

I have also tried using samtools:

samtools faidx CMVrefGenome.fasta

This produces a file called CMVrefGenome.fast.fai in the same directory, however when I try to run the tracy variant calling as above, I still get the error saying the genome is too long or needs to be indexed. I'm completely out of ideas now on how to solve this

Thanks in advance

Answer 1

[trausch]

This should work:

bgzip CMVrefGenome.fasta
samtools faidx CMVrefGenome.fasta.gz
tracy index -o CMVrefGenome.fasta.fm9 CMVrefGenome.fasta.gz
tracy decompose -r CMVrefGenome.fasta.gz ...