Decompose doesn't give bcf file give json instead

[rahulAAI]

tracy decompose -v -o outprefix -g ref.fna Sample.ab1
used this command for variant calling, getting a json file but no bcf

[tobiasrausch]

The genome is specified with -r and not -g. Your command should be:

tracy decompose -v -o outprefix -r ref.fna Sample.ab1

This command generates outprefix.json and outprefix.bcf among other files.

Please also check you are using the latest tracy version (v0.7.1):

tracy -v

[rahulAAI]

Thank you, the version upgrade worked .
but now i am facing a new problem.
tracy index -o ref.fa.fm9 ref.fna
does not produce a ref.fa.fm9 file
i have tried indexing with samtools faidx and the using this command as well
Thank you for your help

[tobiasrausch]

The genome ref.fa needs to be bgzipped (htslib) and indexed with samtools (samtools).

bgzip ref.fa
samtools index ref.fa.gz
tracy index -o ref.fa.fm9 ref.fa.gz