SCReadCount Output

SCReadCounts output files are created based on the output filename provided.

SCReadCounts output file

A tab-separated values file consisting of the computed counts for each SNV locus and cell-bardcode.

CHROM

Chromosome identifier

POS

Chromosome position of the variant

REF

Reference allele nucleotide

ALT

Variant allele nucleotide

ReadGroup

Name of the aligned reads file for the following read counts.

SNVCountForward

Number of forward oriented variant reads in the paired end alignment.

SNVCountReverse

Number of reverse oriented variant reads in the paired end alignment.

RefCountForward

Number of forward oriented reference reads in the paired end alignment.

RefCountReverse

Number of reverse oriented reference reads in the paired end alignment.

SNVCount

Total number of variant reads.

RefCount

Total number of reference reads.

GoodReads

Total number of good reads.

%BadRead

Percentage of bad reads.

VAF

Variant allele fraction

SCReadCounts Counts matrix

File with extention *.cnt.matrix.<extn> for output file with extension *.<extn>. Contains read counts for the reference and alternative allele at each locus and in each cell. Rows represent loci, columns represent cell barcodes. Values are refcnt;altcnt.

SCReadCounts VAF matrix

File with extension *.vaf.matrix.<extn> for output file with extension *.<extn>. Contains variant allele frequency (VAF) for loci with at least the minimum required number of good reads (Min. Reads or -m option) at each locus and in each cell. Rows represent loci, columns represent cell barcodes. Loci and cells without sufficient reads are indicated with NA.