HTML report
Danisov opened this issue · comments
Hi,
I ran both 10 trio, one duo and 11 unrelated samples using bam file.
Two slightly strange things I found in the html report.
1: for the duo it is well placed among parent-child but the point color corresponds to the color as unrelated samples.
2: A female sample, it is well palced among the female samples but the point coloring (gray) is different compared to the others female.
Do you have an idea ??
1: this should not be the case, but you can try adding a fake dad to the kid. e.g. "fakedad". and then add a sample line for the fakedad. e.g.: $fam_id fakedad -9 -9 1 -9. Can you show the lines for the 2 samples?
2: likewise, can you show the line in the pedigree file for this sample?
Hi @brentp
Please find the first line corresponds to the duo (samplaA and sampleB). The second corresponds to the sample long with original sex pedigree unknown (sample1)
family_id sample_id paternal_id maternal_id sex original_pedigree_sex gt_depth_mean gt_depth_sd depth_mean depth_sd ab_mean ab_std n_hom_ref n_het n_hom_alt n_unknown p_middling_ab X_depth_mean X_n X_hom_ref X_het X_hom_alt Y_depth_mean Y_n
sampleA sampleB 1 male 39.6 7.6 39.6 7.6 0.53 0.39 4594 6869 5613 308 0.009 19.78 356 181 0 175 20.33 15
sample1 sample1 unknown 35.6 7.3 35.6 7.4 0.53 0.39 4060 6668 5060 1596 0.071 35.41 341 105 138 98 0.00 0
This line: sampleA sampleB 1 male is a single sample. Where's the other sample in that family? It will need to have the same family id (sampleA) for somalier to match it.
This line: sample1 sample1 unknown shows that there is no sex specified in the column of the pedigree file.
So you just need to update the pedigree file that you send to somalier to include the sex and the include some value for sampleA.
Hi @brentp sorry for the delay of my answe
I used pedigree file obtained by somalier. For a reason of validation of the manipulations within our laboratory, was asked to determine the sex and the relatedness within these samples without having an idea on their sex and real relatedness that's why I used the pedigree file obtained by somalier.
The question I ask myself: is that for the sex and the relatedness was well determined in the pedigree file obtained by somalier with the exception of the samples that I had mentioned
Hi, I'm not able to understand your response.
If you can respond to my previous message point-by-point, perhaps I can help.
Or if I miss a question in your latest, I will attempt to help if you can clarify.