yul96 commented 1 year ago

The ref and alt allele info for the variants are not in the annotated VCF file. Below is an example output

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE

VEC1 6810 . AT A 1.649 PASS DP=1460;DPS=731,729 GT:GQ 1:2 VEC1 7041 . GAG TT 6.674 PASS DP=1266;DPS=636,630 GT:GQ 1:7

Command used: medaka_haploid_variant -i in.fastq.gz -r ref.fasta -o medaka-variant -m r1041_e82_260bps_sup_g632

This information is important to do customized filtering. Is there a way to turn it on? Thanks

SR and SC are described in the header as below

INFO=

cjw85 commented 1 year ago

Please see the command-line help information for the annotate command, specifically the --dpsp option.

It is not recommended to filtered based on these metrics as to do so largely negates the use of medaka as a variant caller.

yul96 commented 1 year ago

Thank you so much! this is helpful. The info is also useful for diagnosis.