readCounts Input Files

SNVs

Single-nucleotide-variants (SNVs) in tabular or VCF format. Tabular formats and their required extensions include whitespace separated text files (.txt), tab-separated values files (.tsv), comma-separated values files (.csv), Excel (.xlsx), and Excel 2003 (.xls).

Text files must have four white-space separated columns representing the chromosome (CHROM), locus (POS), wild-type allele nucleotide (REF), and SNV nucleotide (ALT). Other tabular formats must provide CHROM, POS, REF, ALT headings.

All SNV loci and read alignments must indicate genomic position with respect to the same specific release of a common reference genome.

Read Alignment Files

Read alignment files in indexed BAM format. Filename extension .bam expected with .bam.bai index files in the same folder. readCounts will execute fastest if all BAM files are sorted and indexed in a consistent manner.

All read alignemnts and SNV locimust indicate genomic position with respect to the same specific release of a common reference genome.