HapCompass ManualDerek Aguiar |
HapCompass is a software package for haplotype assembly of diploid, polyploid, and tumor genomes[1,2,3].
HapCompass is a graph-theoretic algorithm for genome-wide haplotype assembly. HapCompass-Polyploidy and HapCompass-Tumor are the first models and algorithms to extend haplotype assembly beyond diploid genomes.
HapCompass can be downloaded from http://www.brown.edu/Research/Istrail_Lab/hapcompass.php.
usage: java [JVM options] -jar hapcompass.jar [OPTIONS]...
Example usage
java -Xmx1g -jar hapcompass.jar –bam example/example.bam –vcf example/62_ID0.txt -o example/out
The parameters to HAPCOMPASS are given in -<parameter> <value> or --<parameter>=<value> pairs if there are arguments or -<parameter> or --<parameter> for boolean switches.
-b,--bam <arg> The BAM or SAM file to process. The
preferred input is a BAM file that is coordinate
sorted. If you require name sorted input files, the
--namesort option may be used in conjunction
with aname sorted BAM or SAM file. If the file is
name sorted, mated reads must has the same name.
-o,--output <arg> Prefix to write output files to. This should
include a reference to the directory and a prefix
for files, for example: /home/me/myOutput_prefix
-v,--vcf <arg> The VCF file VCFFILE giving the variants. The VCF
file should follow the VCF 4.1 standard, that
is,it should have 8 tab delimited columns: #CHROM
POS ID REF ALT QUAL FILTER INFO followed by a
FORMAT column and 1 column representing the
individual's genotypes.
-c,--cache Enable caching of chunks of the input BAM file.
This option is off by default but can be used if
you are experiencing problems with the default
BAM loading and the BAM file is very large with
many very long insert size reads.
-d,--debug Turn on debugging. This option will produce an
output log file.
-e,--export Don't run the algorithm, just export data files.
-f,--fragment <arg> Set input fragment filename.
-g,--downsample <arg> Downsample an input BAM file.
-i,--prim Turn on the Prim-like algorithm for resolution of
the general chain graph for polyploid genomes.
-j,--diverse Force HapCompass to prefer edges in G_C that
include more unique haplotypes. This option
sometimes works well when the coverage is low and
the sequence read length is long.
-l,--suffix <arg> Defines a suffix to trim off read names. This was
added as a convinience for processing some files
produced by sff_extract.
-n,--namesort HapCompass will assume the input SAM/BAM files
are sorted by name
-p,--ploidy <arg> Set the ploidy of the genome to be assembled.
Value must be 2 or higher. Any number above 2
will trigger usage of the polyploid algorithm.
Default is 2
-r,--reference <arg> HapCompass will only produce results from this
reference name. This must match a VCF and SAM/BAM
reference name.
-s,--simulate <arg> HapCompass will simulate reads with properties
given by the string:<number of reads>:<read
length>:<single base error substitution
probability>:<smallest base to sample>:<largest
base to sample>:<list of insert sizes seperated
by commas>:<list of insert sizes seperated by
commas>:<reference name to simulate reads
for>:<only produce good reads>Example:
1000:200:0.01:1:14000:3500,2500:1150,1250:chr1:tr
ue will simulate 1000 paired reads with 200 bases
for each read of the pairs, 1% error rate, in the
region of [1,14000], with insert sizes 3500 and
2500 and insert size standard deviations 1150 and
1250 respectively for reference chr1 and only
produce reads with 2 or more variants
-x,--evaluate <arg> Provide a phasing filename which was output from
HapCompass for evaluation.
-y,--ilp Output ILP file.
-z,--iterations <arg> Number of iterations to run. The larger the value
the more accuracte the assembly. Default is 10
for ploidy = 2, and 1 for ploidy > 2.
Several files will be output to the -o directory.
OUTPUT_PREFIX_<ALGORITHM>_solution.txtBLOCK <start_position_of_block> <end_position> <start_snp_number> <end_snp_number> <score><snp_id> <snp_position> <snp_number> <hap_0_allele> <hap_1_allele>In the case of assembling more than 2 haplotypes, there will be additional columns for the extra haplotypes.
OUTPUT_PREFIX_reduced_representation.vcf andOUTPUT_PREFIX_reduced_representation.samOUTPUT_PREFIX_reads.sam
OUTPUT_PREFIX_binning.txt-ploidy > 2. Contains the pairwise variant phasings defined in the compass graph GC.
OUTPUT_PREFIX_frags.txtThe HapCompass package includes sample files for all types of input.
HapCompass always requires specification of variants in the form of a VCF file. VCF specification can be found https://github.com/amarcket/vcf_spec.
There are two options for inputting sequence reads: BAM and fragment files.
A SAM file is a tab delimited file for specifying sequence reads and their properties. A BAM file is the SAM files binary version. BAM and SAM files may be manipulated using SAMTools. The BAM specification can be found http://samtools.sourceforge.net/SAMv1.pdf.
Fragment files are a tab delimited file format with reads separated by new lines. The columns are specified as follows:
A read part is a space delimited list beginning with a reference name and then a set of one or more position(s), allele(s), base quality score(s) trios.
The position is the 0-based position of the variant in the VCF file. E.g. the first variant is position 0, the second variant is position 1, and so on.
The allele is the numerically encoded allele, 0 for reference, 1 for first alternative allele, and so on.
The base quality score is the ASCII of Phred-scaled base quality+33.
An example of a paired read is given below <tab> denotes a tab character:
2<tab>sequence_read_1<tab>chr1 0 1 D 1 1 D<tab>chr1 4 0 D 5 0 D 6 0 D
HapCompass, and haplotype assembly algorithms in general, requires a set of aligned sequence reads and variants calls. The polyploid algorithm requires knowledge of the number of homologous copies.
Standard genome sequencing workflows produce contiguous DNA segments of an unknown chromosomal origin. De-novo assemblies for genomes with two sets of chromosomes (diploid) or more (polyploid) produce consensus sequences in which the relative haplotype phase between variants is undetermined. The set of sequencing reads can be mapped to the phase-ambiguous reference genome and the diploid chromosome origin can be determined but, without knowledge of the haplotype sequences, reads cannot be mapped to the particular haploid chromosome sequence. However, sequence reads are derived from a single haploid fragment and thus provide valuable phase information when they contain two or more variants. The haplotype assembly problem aims to compute the haplotype sequences for each chromosome given a set of aligned sequence reads to the genome and variant information. The haplotype phase of variants is inferred from assembling overlapping sequence reads.
Derek Aguiar earned his PhD from the Department of Computer Science at Brown University working under the direction of Sorin Istrail.
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