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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
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Somatic Hypermutation Status of IGHV status #1672

Closed xmy1990 closed 3 months ago

xmy1990 commented 3 months ago

Hi,

command, mixcr exportClones -vIdentityPercents -vBestIdentityPercent -dIdentityPercents -dBestIdentityPercent -jIdentityPercents -jBestIdentityPercent test.contigs.clns clones.tsv

clones_IGH.tsv, cloneId readCount readFraction targetSequences targetQualities allVHitsWithScore allDHitsWithScore allJHitsWithScore allCHitsWithScore allVAlignments allDAlignments allJAlignments allCAlignments nSeqFR1 minQualFR1 nSeqCDR1 minQualCDR1 nSeqFR2 minQualFR2 nSeqCDR2 minQualCDR2 nSeqFR3 minQualFR3 nSeqCDR3 minQualCDR3 nSeqFR4 minQualFR4 aaSeqFR1 aaSeqCDR1 aaSeqFR2 aaSeqCDR2 aaSeqFR3 aaSeqCDR3 aaSeqFR4 refPoints vIdentityPercents vBestIdentityPercent dIdentityPercents dBestIdentityPercent jIdentityPercents jBestIdentityPercent

which of the "vIdentityPercents vBestIdentityPercent dIdentityPercents dBestIdentityPercent jIdentityPercents jBestIdentityPercent" can use to evaluate Somatic Hypermutation Status of IGHV status?

Thanks

xmy1990 commented 3 months ago

IGHV status, Somatic Hypermutation Status of immunoglobulin heavy variable (IGHV) genes

mizraelson commented 3 months ago

Hi,

I think the best field is -nMutationsRate VRegionTrimmed. This will give you the number of mutations in the V gene divided by its length. It is recommended to first run mixcr findalleles and then exportClones, as in that case you will have less of a chance of confusing mutations (SHMs) with allelic variants.