multiple reference sequences

Question

[emilydolivo97]

Hello , Can I use freebayes on multiple reference sequences . These reference sequences are merged in one FASTA file and each reference start with ">" if yes , there is a special parameter that I need to add to my command line ? for instance , I 'm only using one reference sequence and for that I'm running this command :

freebayes -f path/ref_sequence -L path/BAM_file --vcf path/variants --ploidy 2 --min-alternate-fraction 0.05

[dthorbur]

It sounds like you need to build and align to a pangenome assembly first, before you can use any of the freebayes functionality. See recent human pangenome paper here that does exactly this.

Appending references together into a single file would probably be very messy, and likely not very informative.