IMGT_V_BY_SEGMENTS is composed of five parts CDR1, CDR2, FWR1, FWR2 and FWR3?

[林显祖]

Hi, I am recently using shazam for SHM analysis. shazam output mutation counts (IMGT_V_BY_SEGMENTS) do not match the MiXCR exported mutation counts (VRegion) results. Confirmed VRegion includes FR1,FR2,FR3,CDR1,CDR2, GemlineVCDR3Part. So I wanted to make sure that IMGT_V_BY_SEGMENTS was not including GemlineVCDR3Part to cause the difference in the results.

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[ssnn]

Hi. Shazam requires IMGT-aligned sequences. IMGT_V_BY_SEGMENTS does not consider the CDR3 region, because it only considers positions up to nucleotide 312. From ?shazam::IMGT_SCHEMES:

IMGT_V_BY_REGIONS: The IMGT numbered V segment up to position nucleotide 312. This defines separate regions for each of CDR1, CDR2, FWR1, FWR2 and FWR3. CDR3 and FWR4 are excluded as they are downstream of nucleotide 312.
IMGT_V_BY_SEGMENTS: The IMGT numbered V segment up to position nucleotide 312. This definition has no subdivisons and treats the entire V segment as a single region.

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