Closed dbolotin closed 7 years ago
Complex issue. For example how to report two consequent substitutions, which are only non-synonymous when present together. Either report them as synonymous or allow to aggregate mutations (milib)
I'm thinking about simplest algorithm:
ATTAAGACACAGATA
|||| |||| ||||
ATTATAACACCGATA
->
ATTAAGACACAGATA
I K T Q I
| | |
I I T P I
ATTATAACACCGATA
->
SK1I, SQ3P
Exceptional cases:
frameshift
)
ATTAAGACACA-GATA
ATTA-GACACATGATA
->
ATTAAGACACAGATA
I K T Q I
| |
I R H M I
ATTAGACACATGATA
->
SK1R, ST2H, SQ3M
Basic feature for this is already implemented in com.milaboratory.core.mutations.MutationsUtil.nt2aa()...
"it is now the case a mixture of SHM and NGS-related"
NGS error should be negligible compared with shm, since 'the mutation occur at a rate of about one muation per V-region sequence per cell division" ?
I am trying to calculated SHM using mixcr.
I use the command
mixcr exportClones -vHit -jHit -dHit -count -aaFeature CDR3 -vAlignment -jAlignment
to export the clone with v j alignment, and calculate the mutation based on alignment. but the shm result is very different from what I get using igblast. (we are switching from igblast to mixcr)
Am I in the right direction? Thanks.
of course, if the shm can be exported directly, it will be great.
From this letter:
Oh well. One more question about the mutations: these are interpretable as SHM, right? Assuming there is not sequencing/pcr error, so NGS being completely error-free, then these mutations would be SHM, and, not as it is now the case a mixture of SHM and NGS-related errors, right? And a suggestion: it would be nice to have them also on the amino acid levels (similar to IMGT).