Documentation for trio eval

[zeeev]

Dear Heng,

Trying out the trio eval tool, it's a great addition.

Can you share the meaning of S/W/H records?

I'm guessing an S is a sequence?

S ctg.000223F 13 0 12 0 0 0
S ctg.000227F 27 3 23 3 3 0
S ctg.356 10 136 3 7 7 128
W 152511 1638448 0.093083
H 267877 1638666 0.163473

[lh3]

The last number on the W-line gives the sWitch error rate. The last number of the H-line gives the Hamming error rate. The first two numbers on the S-line give the paternal (0) and maternal (1) sites for each contig. The last four numbers give the number of 00, 01, 10 and 11 transitions.

[gsarah]

Hello,
It seems to me that the answer to the mentionned issue is incomplete.
I have the same question. I used yak triobin to obtain the reads used by hifiasm for each haplotype.
I have this table as result:

m64071_201031_183434/10/ccs	m	0	6156	0	6495	0	10	15137	58
m64071_201031_183434/13/ccs	m	0	1445	0	1561	9	28	14360	349
m64071_201031_183434/14/ccs	p	470	0	533	24	1	139	18263	259
m64071_201031_183434/29/ccs	p	1716	0	2508	3	243	87	18602	2554
m64071_201031_183434/38/ccs	p	186	0	349	25	94	24	15667	599
m64071_201031_183434/39/ccs	m	0	8013	0	8109	0	5	15197	188
m64071_201031_183434/40/ccs	p	2612	0	3779	0	0	14	17954	153
m64071_201031_183434/42/ccs	m	0	3441	10	4216	141	147	15287	1492

I guess i can obtain my paternal reads with seqtk using the read id where the second column is tagged as p. Same for the maternal reads with tag m. What does a and 0 stand for in the second column?
Can you describe the other fields?

[lh3]

a=ambiguous, meaning there are strong supports from both parental haplotypes. 0=none, meaning there are no parent-specific k-mers.