Song Cao
mapping reference allele and variant allele to 10X barcodes from an input of scRNA-seq bam and the unique 10X barcode corresponds to each individual cell
usage:
step 1: extracting reads contains the reference allele and variant allele of a somatic variant
perl 10Xmapping.pl --mapq --bam --maf --out
mapq: the mapping quality; Default 0
bam: the scRNA-seq bam path
maf: the maf file containing a list of somatic variants
out: the output file
step 2: get the corresponding table between ref allele, var allele and 10X barcode
perl parse_scrna_bc.pl $fin $fout
fin: the input file from step 1's output
fout: the output file
step 3: output number of reads supporting reference and variant alleles and VAF
perl rc.pl $fin $fout
fin: the input file from step 1's output
fout: the output file