The “seqz” file is produced by sequenza-utils and
typically has the file extension .seqz. The data here is
representative of a seqz file derived from an exome-sequenced tumor sample,
such as could be obtained from TCGA.
data(example.seqz)A data frame with 53937 rows and 14 columns:
| [,1] | chromosome | Chromosome name |
| [,2] | position | Base position |
| [,3] | base.ref | Base in the reference genome |
| [,4] | depth.normal | Read depth in the normal sample |
| [,5] | depth.tumor | Read depth in the tumor sample |
| [,6] | depth.ratio | Ratio of depth.tumor and depth.normal |
| [,7] | Af | A-allele frequency in the tumor sample |
| [,8] | Bf | B-allele frequency in the tumor sample, in heterozygous positions only |
| [,9] | zygosity.normal | Zygosity of the normal sample: "hom" for homozygous or "het" for heterozygous |
| [,10] | GC.percent | % GC content |
| [,11] | good.reads | Number of reads from the tumor sample which pass the quality threshold |
| [,12] | AB.normal | Base(s) found in the normal sample, sorted by allele frequency if more than one |
| [,13] | AB.tumor | Base(s) found in the tumor sample but not in the normal specimen, with their observed frequencies, separated by colons |
| [,14] | tumor.strand | Identical to AB.tumor but indicating, for
each variant base, the fraction of reads
oriented 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.