Output record of fixes

[christopher-holt]

Is there a way to output a record of fixes made by racon (similar to --changes in pilon)?

[isovic]

Hi @christopher-holt ,

You can try out the liftover branch.
It has a couple of new useful features, some seem to be what you are looking for:

        -L, --liftover <string>
            default: ''
            optional prefix of the output liftover files which convert
            the draft sequence to the output consensus. PAF and VCF files
            are always written with this prefix, and SAM can optionally
            be written if the -S option is provided.
        -S, --liftover-sam
            Used only in combination with the -L option, this writes out
            a SAM formatted alignment of the polished sequences vs the draft.
        -B, --bed <str>
            default: ''
            path to a BED file with regions to polish

Important note: diffs reported by the liftover feature are not extracted directly from the POA graph, but are instead obtained from polished-to-draft sequence alignment, so there may be slight difference (but most likely insignificant).

Hope this helps,
Best regards,
Ivan.

[Anees-caas]

@christopher-holt @isovic While installing the racon-liftover, I am facing an issue. Failed to connect to github.com port 443: Connection timed out. I need a VCF file after the Racon polish to run Merfin --polish. The FASTA that I get from the Racon is not compatible with marfin --input .vcf. Please need your guidance