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:false ]

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

seqz

meta

:map

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

*.gz

:file

Seqz file

*.{seqz.gz}

versions

versions.yml

:file

File containing software versions

versions.yml

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
maintainer
Github user kaurravneet4123
get in touch
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