No pedigree inference in samples from same family

[mjlarsen]

Hi In my output from somalier on 4 related individuals (illumina wgs data), i do not get any pedigree inference, as described in https://github.com/brentp/somalier/wiki/pedigree-inference What am I missing ?

for f in *.g.vcf.gz; do
    somalier extract -d extracted/ --sites $sites -f $reference $f
done

somalier relate extracted/*.somalier -o somalier_i -i 

[brentp]

Hi, the output in the html file is always colored by the --ped given, even with inference. So, after inference to see the output in the html, you must re-run somalier relate with --ped somalier_i.samples.txt where somalier_i.samples.txt was created on your first run of somalier relate

If the samples.txt file does not contain any inferred relations, then we must have another problem. Let me know and we can debug further.