Helper scripts to process clone tables from MiXCR
Only dependency is R package optparse.
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Combine two clones tables (e.g. clones_IGL.tsv and clones_IGK.tsv)
The readFraction and/or uniqueUMIFraction is recalculated for the merged table
Rscript combine-clone-tables.R -x $table1 -y $table2 -o $combinedTable
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Collapse clones by VDJ and CDR3 nucleotide sequence
Collapsed clone table has columns: VDJ, nSeqCDR3, readCount (or uniqueUMICount), cloneFraction
Rscript collapse-clone-tables-by-VDJ-CDR3.R -i $infile -o $outfile