Hi! I found this function in the experimental section and I am interested to use phase_trio_matrix_by_transmission. Let’s say I have a MatrixTable with three samples in “s” loaded in the “child, father, mother” order, will I be able to run the function with the mt as the sole argument?
hl.missing was added somewhat recently to replace the deprecated hl.null. What version are you running?
Thank you for your response. This is the version I am running:
I am using Hail on my institution’s cluster. What version would I need?
Is there any way to get around this issue by changing hl.missing to hl.null in the function?
If you changed all the hl.missing to hl.null, that’d probably work, assuming no other new errors crop up.
Your best bet would be updating to latest version of hail though.
Thank you! It worked without any issues. However, all of my entries only show the proband. This is my trio information:
However, when I try father_entry.GT.show() or mother_entry.GT.show(), I get the genotype information for the proband:
This is the same for the phased_trio_dataset. Is there any way to resolve this? Thank you so much.
This is an incorrect interpretation – the H_VT-8169 is the column key, but each column isn’t a sample, it’s a trio. The column is keyed by the proband identifier. When you show() an entry field of a matrix table, you see the row and column keys too. Here you’re showing the father_entry genotype, but it’s printing out the associated proband ID.
Oh, thank you for the interpretation! What would be the appropriate command to show the GT of PBT_GT for the father and mother?
What’s PBG_GT?
I think perhaps one thing you could try is trio_dataset.entries().show()
entries() is the coordinate-represented table produced from a matrix table – so showing this will print out one line per entry in the matrix table, left to right, top to bottom.
That makes sense! Is it possible to count how many “NA” are there in each of the proband_entry.PBT_GT column? I want to check how many variants were phased out of all variants.