JULIETFLOW.md

julietflow - Minor variant pipeline

Install

Install the minorseq suite using bioconda, more info here. The script is called julietflow.

Input data

Julietflow operates on unaligned ccs reads in the BAM format and a close reference sequence. BAM files have to PacBio-compliant, meaning, cigar M is forbidden, and input reads have to be greater RQ 0.99.

Scope

Current scope of julietflow is automatization of the re-align workflow for minor variant calling.

Output

Julietflow provides the html output of juliet in the current directory and the intermediate files in tmp/ if -k is set.

Filtering

Juliet relies on high-quality input data, please filter your ccs data and downsample it to 6000x:

INPUT=yourdata.ccs.bam
OUTPUT=yourdata.filtered.ccs.bam
samtools view -H ${INPUT} > ${INPUT}.tmp
samtools view ${INPUT} | grep "rq:f:0.99\|rq:f:1" >> ${INPUT}.tmp
samtools view -bS ${INPUT}.tmp > ${OUTPUT}

Example

julietflow -i m530526.ccs.bam -r hxb2.fasta

Output: m530526_cleric.html

Dependencies

All dependencies are automatically installed.

Help

Please use --help for more options of julietflow.

Workflow