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Introduction ============ Lapels remaps reads aligned to the in silico genome back to the reference coordinate and annotates variants. Two files are taken as input: (1) a MOD file that is used to generate the in silico genome and (2) a BAM file that contains the in silico genome alignments. Lapels will generate a new BAM file with corrected read positions, adjusted cigar strings, and annotated tags of variants (eg. SNPs, Insertions, and Deletions). For detail usage, please type after installation: pylapels -h System Requirements =================== Lapels and its modules have been tested under Python 2.6.5 and 2.7 Several python modules are required to run the code. * [pysam >= 0.6] As a wrapper of Samtools, the pysam module facilitates the manipulation of SAM/BAM files in Python. Its latest package can be downloaded from: http://code.google.com/p/pysam/ The current pysam (v0.6) has been reported to have a bug in dealing with integer tags. (http://code.google.com/p/pysam/issues/detail?id=101) A fixed version is provided below. http://www.csbio.unc.edu/~sphuang/pysam/pysam-0.6-devel.tar.gz * [argparse >= 1.2] The argparse module is used to parse the arguments of the module. It has been maintained in Python Standard Library since Python 2.7. It can be found in: http://code.google.com/p/argparse/ . * others Reads that have multiple alignments are required to have tag HI to specify the hit index. Recent aligners (eg. bowtie >= 0.12.8 and tophat >= 1.4.0) will create this tag. It is recommended to use a recent version for read alignment. Installation ============ It is recommended to use easy-install (http://packages.python.org/distribute/easy_install.html) for the installation. Users need to download the tarball of source from http://code.google.com/p/lapels/ and then type: easy_install lapels-<version>.tar.gz By default, the package will be installed under the directory of Python dist-packages, and the executable of pylapels can be found under /usr/local/bin/ . If you don't have permission to install it in the system-owned directory, you can install it in locally following the next steps: (1) Create a local package directory for python: mkdir -p <local_dir> (2) Add the absolute path of <local_dir> to the environment variable PYTHONPATH: export PYTHONPATH=$PYTHONPATH:<local_dir> (3) Use easy_install to install the package in that directory: easy_install -d <local_dir> lapels-<version>.tar.gz For example, if you want to install the package under the home directory in a Linux system, you can type: mkdir -p /home/$USER/.local/lib/python/dist-packages/ export PYTHONPATH=$PYTHONPATH:/home/$USER/.local/lib/python/dist-packages/ easy_install -d /home/$USER/.local/lib/python/dist-packages/ lapels-<version>.tar.gz After installation, pylapels will locate in /home/$USER/.local/lib/python/dist-packages/ . Example ======= Examples can be downloaded from http://code.google.com/p/lapels/ To run on the example files, type: pylapels examples/example.mod examples/example.bam The following is the content in the input and output BAM file in the example (the sequence and mapping quality are omitted). input: UNC9-SN296_0254:3:1305:8580:174183#TGACCA 163 chr2 6361064 255 100M = 6361092 128 <SEQ> <MAPQ> NM:i:1 NH:i:1 UNC9-SN296_0254:3:1305:8580:174183#TGACCA 83 chr2 6361092 255 100M = 6361064 -128 <SEQ> <MAPQ> NM:i:1 NH:i:1 output: UNC9-SN296_0254:3:1305:8580:174183#TGACCA 163 chr2 6363700 255 35M7D63M1I1M = 6363728 134 <SEQ> <MAPQ> NH:i:1 OC:Z:100M OM:i:1 d0:i:7 i0:i:1 s0:i:1 UNC9-SN296_0254:3:1305:8580:174183#TGACCA 83 chr2 6363728 255 7M7D63M1I29M = 6363700 -134 <SEQ> <MAPQ> NH:i:1 OC:Z:100M OM:i:1 d0:i:7 i0:i:1 s0:i:1 In the output, read positions and cigar strings are in the reference coordinate. The length of each read(template) and the mate position (if any) has been updated. New tags have been added for each read. The default tags and their meaning are shown below: OC : the old cigar in the alignment of the in silico genome OM : the old NM (edit distance to the in silico sequence) s0 : the number of observed SNP positions having the in silico alleles i0 : the number of bases in the observed insertions having in silico alleles d0 : the number of bases in the observed deletions having in silico alleles Auxiliary Tools =============== vcf2mod convert an VCF file into a MOD file insilico construct the pseudo genome from a MOD file and a reference FASTA file fixmate fix the mate information (a replacement of samtools fixmate) Please refer to their help information (-h) for detail usage.
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