Description

Annotate aligned Long-C monomer BAM records: group alignments by concatemer read, order monomers, and assign fragment tags (FI, FD, BX) for downstream pairtools parsing.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

bam (file)

Coordinate- or name-sorted aligned BAM from minimap2

*.bam

bai (file)

BAM index

*.bam.bai

Output

Name
Description
Pattern

bam

meta (map)

Groovy Map containing sample information

*.bam (file)

Annotated, coordinate-sorted BAM with FI, FD, and BX tags

*.bam

index

meta (map)

Groovy Map containing sample information

*.bam.bai (file)

BAM index

*.bam.bai

versions_python

${task.process} (string)

The process the versions were collected from

python (string)

The tool name

python -c "import sys; print(sys.version.split()[0])" (eval)

The expression to obtain the version of the tool

versions_annotate_frag

${task.process} (string)

The process the versions were collected from

annotate_frag.py (string)

The tool name

annotate_frag.py --version | sed 's/^.* //' (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The process the versions were collected from

python (string)

The tool name

python -c "import sys; print(sys.version.split()[0])" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The process the versions were collected from

annotate_frag.py (string)

The tool name

annotate_frag.py --version | sed 's/^.* //' (eval)

The expression to obtain the version of the tool

Tools

annotate_frag.py Documentation

Group alignments by read ID, filter by MAPQ, order monomers, and write FI/FD/BX BAM tags.

License: MIT
Authors