AlignStats produces various alignment, whole genome coverage, and capture
coverage metrics for sequence alignment files in SAM, BAM, and CRAM format.
This program is designed to serve reporting and quality control purposes in
sequencing analysis pipelines at the Baylor College of Medicine Human Genome
Sequencing Center (BCM-HGSC). Descriptions of reported metrics can be found in
doc/.
AlignStats requires a recent version of HTSlib (versions 1.3 and higher are
known to work, version 1.4 or higher is suggested). The -p option for
multithreading requires libpthread support.
To build AlignStats, run:
autoconf
./configure
make
AlignStats multithreading support is enabled by running configure as:
./configure --enable-multithreading
alignstats [-i INPUT] [-j FORMAT] [-o OUTPUT]
[-h] [-v] [-n NUMREADS] [-p] [-P INT]
[-r REGIONS] [-t TARGET] [-m COVMASK] [-T REFFASTA]
[-q INT] [-f INT] [-F INT]
[-D] [-U] [-A] [-C] [-W]
Runtime options:
-h Print usage information.
-v Print verbose runtime information output to stderr.
-n INT Maximum number of records to keep in memory.
-p Use separate threads for reading and processing records
(requires builtin pthread support).
-P INT Number of HTSlib decompression threads to spawn.
File options:
-i INPUT Read INPUT as the input SAM, BAM, or CRAM file (stdin). Input
must be coordinate-sorted for accurate results.
-j FORMAT Specify file format of input alignment file ("sam", "bam", or
"cram" available, default guessed from filename or "sam").
-o OUTPUT Write report to OUTPUT (stdout).
-r REGIONS File in BED format listing which regions to process. By
default, all available records are processed. This option
requires the alignment file to be indexed.
-t TARGET File in BED format listing capture coverage regions. Required
if capture coverage statistics are enabled.
-m COVMASK File in BED format listing regions of N bases in reference.
Coverage counts will be suppressed for these regions.
-T REFFASTA Indexed FASTA reference file for CRAM input alignment.
Processing options:
-q INT Only process records with minimum read quality of INT.
-f INT Only process records with all bits in INT set in FLAG.
-F INT Only process records with none of bits in INT set in FLAG.
Reporting options:
-D Disable excluding duplicate reads from coverage statistics.
-U Disable processing unplaced unmapped reads (CHROM "*") when
using the -r option.
-A Disable reporting alignment statistics.
-C Disable reporting capture coverage statistics.
-W Disable reporting whole genome coverage statistics.
alignstats -i sample.bam -o report.txt -r regions.bed -t targets.bed -m n_regions.bed
Run AlignStats with sample.bam as the input alignment file,
regions.bed as the input regions file, targets.bed as the input target
file, n_regions.bed as the input coverage mask file, and report.txt as
the output report file. Both whole genome and capture statistics will be
produced for coverage metrics.
alignstats -v -p -i sample.bam -r regions.bed -t targets.bed -m n_regions.bed -o report.txt
Run the first command in verbose mode and enable multithreading (if supported).
alignstats -i sample.bam -r regions.bed -t targets.bed -m n_regions.bed
Same as the first command, but the report will be printed to stdout.
alignstats -C -i sample.bam -o report.txt
Only produce alignment statistics and whole genome coverage statistics
(suppress capture coverage statistics) for sample.bam.
While extensive testing and validation have been performed at the BCM-HGSC to confirm the accuracy of metrics reported by AlignStats, no guarantees of accuracy are made or implied.
The set of metrics reported by AlignStats may change in the course of continued development by the BCM-HGSC.
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