The “seqz” file is produced by sequenza-utils.py and typically has the file extension .seqz. The data here is representative of an exome-sequenced tumor sample, such as could be obtained from TCGA.
data(example.seqz)A data frame with a header row and 13 columns:
with the chromosome name
with the base position
with the base in the reference genome used (usually hg19). Note the base.ref is NOT necessarily the base in the normal specimen.
read depth observed in the normal sample
read depth observed in the tumor sample
ratio of depth.tumor and depth.normal
A-allele frequency observed in the tumor sample
B-allele frequency observed in the tumor sample in heterozygous positions
zygosity of the reference sample. "hom" corresponds to AA or BB, whereas "het" corresponds to AB or BA
GC-content (percent), calculated from the reference genome in fixed nucleotide windows
number of reads that passed the quality threshold (threshold specified in the pre-processing software), in the tumor specimen
base(s) found in the germline sample; for heterozygous positions AB are sorted using the values of Af and Bf respectively
base(s) found in the tumor sample not present in the normal specimen. The field include all the variants found in the tumor alignment, separated by a colon. Each variant contains the base and the observed frequency
frequency of the variant nucleotides detected on the forward orientation. The field have a consistent structure with AB.tumor, indicating the fraction, relative to the total number of reads presenting the specific variant, orientated in the forward direction
example.seqz can be loaded in the standard R way via data(example.seqz), or it can be read from a text file using read.seqz. The former is useful for examples and testing, whereas the latter is representative of the standard workflow.