SNPlice Input Files
Read Alignments
Read alignments in (indexed) BAM/SAM format. Filename extension .bam expected, with .bam.bai index files.
Junctions
Exon-intron-exon junctions in BED format. Filename extension .bed expected.
Junctions are represented as two exon “blocks” separated by an intron, as output by TopHat’s junction output option.
SNPs
Single-nucleotide-polymophisms (SNPs) in tabular and VCF format. Tabular formats/extensions include txt, tsv, csv, xlsx, xls.
Text files (txt) must have four white-space separated columns representing the chromosome (CHROM), locus (POS), wild-type allele nucleotide (REF), and SNP nucleotide (ALT). Other tabular formats must provide CHROM, POS, REF, ALT headings. Extra values in tabular or VCF format files are mapped to the output.