Comments (3)
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.
from yak.
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?
from yak.
a
=ambiguous, meaning there are strong supports from both parental haplotypes. 0
=none, meaning there are no parent-specific k-mers.
from yak.
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from yak.