README.md

BamTools

Various routines to run on a BAM file

BamMetrics

Capture BAM metrics

Usage

java -cp bam-tools.jar com.hartwig.hmftools.bamtools.metrics.BamMetrics \
   -bam_file SAMPLE.bam \
   -ref_genome ref_genome.fasta \
   -output_dir /output_dir/ \
   -threads 10 \

Configuration

Filter	Description
sample	Optional sample ID, used to set output filenames
bam_file	BAM file to analyse
ref_genome	Reference genome file used to create the BAM
ref_genome_version	Reference genome version, V37 (default) or V38
regions_bed_file	Optional BED file to restrict the sections of the genome analysed
specific_regions	Optional list of regions to analyse. Format 'chr:posStart-posEnd; etc'
write_old_style	Write a single output file with same format to Picard CollectWgsMetrics for compatibility
output_dir	Path for output file(s)
log_level	INFO or DEBUG
threads	Multi-thread count, default 1
partition_size	Default 1M bases, splits chromosomes to analyse in partitions
map_qual_threshold	Reads below this map quality count towards MAPQ counts, default 20
base_qual_threshold	Bases below this base quality count towards BASEQ count, default 10
max_coverage	Positions with coverage above this count towards CAPPED counts, default 250

RegionSlicer

Slice a BAM and gather remote mate and supplementary reads

Usage

java -cp bam-tools.jar com.hartwig.hmftools.bamtools.slice.RegionSlicer \
   -bam_file SAMPLE.bam \
   -output_prefix 
   -ref_genome ref_genome.fasta \
   -specific_regions 
   -output_dir /output_dir/ \
   -threads 10 \

Configuration

Filter	Description
bam_file	BAM file to slice
output_prefix	Use in file output
ref_genome	Reference genome file used to create the BAM
regions_file	Optional BED file to restrict the sections of the genome analysed
partition_size	Default 1M bases, splits chromosomes to analyse in partitions
specific_regions	Optional list of regions to analyse. Format 'chr:posStart-posEnd; etc'
write_reads	Write reads to TSV file
drop_remote_supps	Ignore remote supplementary reads
output_dir	Path for output file, if omitted will write to same directory as BAM file
log_level	INFO or DEBUG
threads	Multi-thread count, default 1

BamCompare

Compare 2 BAM/CRAM files and write differences into a TSV file.

Usage

java -cp bam-tools.jar com.hartwig.hmftools.bamtools.compare.BamCompare \
   -orig_bam_file SAMPLE.original.bam \
   -new_bam_file SAMPLE.new.bam \
   -ref_genome ref_genome.fasta \
   -output_file SAMPLE.bam_compare.tsv.gz \ 
   -threads 10 \

Configuration

Filter	Required?	Description
orig_bam_file	Yes	First BAM / CRAM file
new_bam_file	Yes	Second BAM / CRAM file
ref_genome	No	Reference genome file, only required for CRAM input.
output_file	Yes	Output comparison file (tsv or tsv.gz)
ignore_dup_diffs	No	Ignore difference in duplicate flag
ignore_alterations	No	Ignore consensus reads and internal unmappings
ignore_consensus_reads	No	Ignore consensus reads
ignore_supplementary_reads	No	Ignore supplementary reads
partition_size	No	Default 10M bases, splits chromosomes to analyse in partitions
max_cached_reads_per_thread	No	Maximum number of cached reads per thread, automatically calculated if not set
specific_regions	No	As above
log_level	No	WARN, INFO, DEBUG or TRACE
threads	No	Multi-thread count, default 1

BamToFastq

Convert BAM / CRAM file into FASTQ

Usage

java -cp bam-tools.jar com.hartwig.hmftools.bamtools.tofastq.BamToFastq \
   -bam_file SAMPLE.cram \
   -ref_genome ref_genome.fasta \
   -output_dir /output \
   -split_mode READ_GROUP \ 
   -threads 10 \

Configuration

Filter	Required?	Description
bam_file	Yes	input BAM / CRAM file
ref_genome	No	Reference genome file, only required for CRAM input.
output_dir	Yes	Directory to write output into.
output_id	No	Extra file name prefix for the output FASTQ files
split_mode	No	How output FASTQ files are split (NONE, READ_GROUP, THREAD)
specific_regions	No	As above
log_level	No	WARN, INFO, DEBUG or TRACE
threads	No	Multi-thread count, default 1

Version History and Download Links

• 1.0