Description

Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

normalbam (file)

BAM file from the reference/normal sample

*.{bam}

tumourbam (file)

BAM file from the tumour sample

*.{bam}

fasta (file)

Reference FASTA file

*.{fasta}

wigfile (file)

GC content wiggle file

*.{wig.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

seqz (file)

Seqz file

*.{seqz.gz}
maintainer
Github user kaurravneet4123
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Tools

sequenzautils
GPL-3.0-or-later

Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.

sequenza-utils.readthedocs.io/en/latest 10.1093/annonc/mdu479