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these sequences are also translated into predicted protein haplotype sequences. Each variant haplotype sequence is aligned and compared to the reference, and an HGVS-like name is constructed representing its differences to the reference.</p> <p>This approach offers an advantage over VEP's analysis, which treats each input variant independently. By considering the combined change contributed by all the variant alleles across a transcript, the compound effects the variants may have are correctly accounted for.</p> <p><b>haplo</b> shares much of the same command line functionality with vep, and can use VEP caches, Ensembl databases, GFF and GTF files as sources of transcript data; all vep command line flags relating to this functionality work the same with <b>haplo</b>.</p> <br /> <h2 id="hp_dl_install">Download and install</h2> <p><b>Haplosaurus</b> is part of the <a href="https://github.com/Ensembl/ensembl-vep/blob/release/113/haplo" rel="external">VEP package</a>.</p> <p>Please follow the instructions about the <img src="/i/16/download.png" style="vertical-align:middle"/> <a href="/info/docs/tools/vep/script/vep_download.html">download and installation of VEP</a>.</p> <div> <div style="float:left" class="info"> <h3 id="limitations">Getting Haplosaurus to run faster</h3> <div class="message-pad"> <p> Haplosaurus can run faster (and in some cases with less memory), using a compiled alignment algorithm from the <b>bioperl-ext</b> package.<br /> <b>bioperl-ext</b> is not part of the default VEP installation as it is only used by Haplosaurus, however we recommend to install it.<br /> See the detailed installation instructions of this package <a href="#hp_bioperl_ext">here</a>. </p> </div> </div> <div class="clear"></div> </div> <br /> <h2 id="hp_usage">Usage</h2> <p>Input data must be a <b>VCF containing phased genotype data for at least one individual</b> and file must be sorted by chromosome and genomic position; no other formats are currently supported.</p> <p>Example of VCF input:<p/> <pre class="code sh_sh">##fileformat=VCFv4.2 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT IND1 IND2 12 6029429 rs1800380 C T . . . GT 1|0 1|0 12 6029431 rs370984712 G A . . . GT 1|0 1|0 12 12477741 rs201941751 GCACGC G . . . GT 0|1 1|0 12 12477747 rs200271649 TGGGC T . . . GT 0|1 1|0 21 25597309 rs540774105 G A . . . GT 0|0 0|0 21 25597391 rs1135618 T C . . . GT 1|1 1|0 21 25606638 rs3989369 A G . . . GT 0|1 0|0</pre> <p>When using a VEP cache as the source of transcript annotation, the first time you run haplo with a particular cache it will spend some time scanning transcript locations in the cache.</p> <pre class="code sh_sh">./haplo -i input.vcf -o out.txt --cache</pre> <br /> <h2 id="hp_output">Output</h2> <p>The default output format is a simple tab-delimited file reporting all observed non-reference haplotypes. It has the following fields:</p> <ol> <li>Transcript stable ID</li> <li>CDS haplotype name</li> <li>Comma-separated list of flags for CDS haplotype</li> <li>Protein haplotype name</li> <li>Comma-separated list of flags for protein haplotype</li> <li>Comma-separated list of frequency data for protein haplotype</li> <li>Comma-separated list of contributing variants</li> <li>Comma-separated list of sample:count that exhibit this haplotype</li> </ol> <p>Example of outputs (default format), using the VCF data displayed above:</p> <pre class="code sh_sh"># Input #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT IND1 IND2 12 6029429 rs1800380 C T . . . GT 1|0 1|0 12 6029431 rs370984712 G A . . . GT 1|0 1|0 # Output ENST00000261405 | ENST00000261405:<b>2878C>T,2880G>A</b> | | ENSP00000261405:<b>960R>*,961del{1854}</b> | <b>stop_change</b> | | rs370984712,rs1800380 | IND1:1,IND2:1</pre> <pre class="code sh_sh"># Input #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT IND1 IND2 12 12477741 rs201941751 GCACGC G . . . GT 0|1 1|0 12 12477747 rs200271649 TGGGC T . . . GT 0|1 1|0 # Output ENST00000298573 | ENST00000298573:<b>1080del{4},1085delG,1087delGTG,1092delC</b> | <b>resolved_frameshift</b>,<b>indel</b> | ENSP00000298573:<b>364delPSV</b> | <b>indel</b> | | rs200271649,rs201941751 | IND1:1,IND2:1</pre> <pre class="code sh_sh"># Input #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT IND1 IND2 21 25597391 rs1135618 T C . . . GT 1|1 1|0 21 25606638 rs3989369 A G . . . GT 0|1 0|0 # Output ENST00000352957 | ENST00000352957:<b>91T>C,612A>G</b> | | ENSP00000284967:<b>31S>P</b> | | | rs3989369,rs1135618 | IND1:1<hr style="border-top:1px solid #CCC;height:1px;margin:5px 0px"/>ENST00000307301 | ENST00000307301:<b>612A>G</b> | | ENSP00000305682:<b>REF</b> | | | rs1135618 | IND1:1,IND2:1 ENST00000307301 | ENST00000307301:<b>91T>C,612A>G</b> | | ENSP00000305682:<b>31S>P</b> | | | rs3989369,rs1135618 | IND1:1<hr style="border-top:1px solid #CCC;height:1px;margin:5px 0px"/>ENST00000419219 | ENST00000419219:<b>582A>G</b> | | ENSP00000404426:<b>REF</b> | | | rs1135618 | IND1:1,IND2:1 ENST00000419219 | ENST00000419219:<b>91T>C,582A>G</b> | | ENSP00000404426:<b>31S>P</b> | | | rs3989369,rs1135618 | IND1:1</pre> <p>Alternatively, JSON output matching the format of the transcript haplotype REST endpoint may be generated by using <b>--json</b>.</p> <p>Each transcript analysed is summarised as a JSON object written to one line of the output file.</p> <p>You may exclude fields in the JSON from being exported with <b>--dont_export field1,field2</b>.<br />This may be used, for example, to exclude the full haplotype sequence and aligned sequences from the output with <b>--dont_export seq,aligned_sequences</b>.</p> <div> <div style="float:left" class="info"> <h3 id="limitations">Note</h3> <div class="message-pad"> <p>JSON output does not currently include side-loaded frequency data.</p> </div> </div> <div class="clear"></div> </div> <br /> <h2 id="hp_rest">REST API</h2> <p>The <a href="https://rest.ensembl.org/documentation/info/transcript_haplotypes_get">transcript haplotype REST endpoint</a> returns arrays of protein_haplotypes and cds_haplotypes for a given transcript.</p> <p>The default haplotype record includes:</p> <ul> <li><b>population_counts</b>: the number of times the haplotype is seen in each population</li> <li><b>population_frequencies</b>: the frequency of the haplotype in each population</li> <li><b>contributing_variants</b>: variants contributing to the haplotype</li> <li><b>diffs</b>: differences between the reference and this haplotype</li> <li><b>hex</b>: the md5 hex of this haplotype sequence</li> <li><b>other_hexes</b>: the md5 hex of other related haplotype sequences (CDSHaplotypes that translate to this ProteinHaplotype or ProteinHaplotype representing the translation of this CDSHaplotype)</li> <li><b>has_indel</b>: does the haplotype contain insertions or deletions</li> <li><b>type</b>: the type of haplotype - cds, protein</li> <li><b>name</b>: a human readable name for the haplotype (sequence id + REF or a change description)</li> <li><b>flags</b>: [flags](#haploflags) for the haplotype</li> <li><b>frequency</b>: haplotype frequency in full sample set</li> <li><b>count</b>: haplotype count in full sample set</li> </ul> <p>The REST service does not return raw sequences, sample-haplotype assignments and the aligned sequences used to generate differences by default.</p> <br /> <h2 id="hp_flags">Flags</h2> <p>Haplotypes may be flagged with one or more of the following:</p> <ul> <li><b>indel</b>: haplotype contains an insertion or deletion (indel) relative to the reference.</li> <li><b>frameshift</b>: haplotype contains at least one indel that disrupts the reading frame of the transcript.</li> <li><b>resolved_frameshift</b>: haplotype contains two or more indels whose combined effect restores the reading frame of the transcript.</li> <li><b>stop_changed</b>: indicates either a STOP codon is gained (protein truncating variant, PTV) or the existing reference STOP codon is lost.</li> <li><b>deleterious_sift_or_polyphen</b>: haplotype contains at least one single amino acid substitution event flagged as deleterious (SIFT) or probably damaging (PolyPhen-2).</li> </ul> <br /> <h2 id="hp_bioperl_ext">bioperl-ext</h2> <p><b>haplo</b> can make use of a fast compiled alignment algorithm from the <a href="https://github.com/bioperl/bioperl-ext">bioperl-ext</a> package; this can speed up analysis, particularly in longer transcripts where insertions and/or deletions are introduced.</p> <p><b>The bioperl-ext package is no longer maintained and requires some tweaking to install.</b></p> <p>The following instructions install the package in <b>$HOME/perl5</b>; edit <b>PREFIX=[path]</b> to change this. You may also need to edit the <b>export</b> command to point to the path created for the architecture on your machine.</p> <pre class="code sh_sh">git clone https://github.com/bioperl/bioperl-ext.git cd bioperl-ext/Bio/Ext/Align/ perl -pi -e"s|(cd libs.+)CFLAGS=\\\'|\$1CFLAGS=\\\'-fPIC |" Makefile.PL perl Makefile.PL PREFIX=~/perl5 make make install cd - export PERL5LIB=${PERL5LIB}:${HOME}/perl5/lib/x86_64-linux-gnu/perl/5.22.1/</pre> <p>If successful the following should print <b>OK</b>:</p> <pre class="code sh_sh">perl -MBio::Tools::dpAlign -e"print qq{OK\n}"</pre> <br /> <h2 id="hp_pub">Publication</h2> <div style="float: left; margin-bottom: 20px; width: 1000px;" class="info"><h3>Haplosaurus</h3> <div class="message-pad"><p> William Spooner, William McLaren, Timothy Slidel, Donna K. Finch, Robin Butler, Jamie Campbell, Laura Eghobamien, David Rider, Christine Mione Kiefer, Matthew J. Robinson, Colin Hardman, Fiona Cunningham, Tristan Vaughan, Paul Flicek and Catherine Chaillan Huntington<br> <strong>Haplosaurus computes protein haplotypes for use in precision drug design.</strong><br> <em>Nature Communications</em> 9:4128(2018)<br> <a href="https://doi.org/10.1038/s41467-018-06542-1" rel="external">doi:10.1038/s41467-018-06542-1</a> </p></div> </div> </div> </div></div> </div> <div id="footer"> <div class="column-wrapper"> <div class="column-two left"> <p>Ensembl release 113 - October 2024 © <span class="print_hide"><a href="http://www.ebi.ac.uk/" class="nowrap constant">EMBL-EBI</a></span> <span class="screen_hide_inline">EMBL-EBI<br />http://useast.ensembl.org</span> </p> </div> <div class="column-two right print_hide"><p> <a class="modal_link" id="p_link" href="/Help/Permalink?url=http%3A%2F%2FOct2024.archive.ensembl.org">Permanent link</a> </p></div> <p class="invisible">.</p> </div> <div class="column-wrapper"><hr /><div id="fat-footer"> <div 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value=Vombatus_ursinus|Sus_scrofa_pietrain|Gambusia_affinis|Castor_canadensis|Sus_scrofa_wuzhishan|Mus_spretus|Moschus_moschiferus|Oryzias_latipes|Propithecus_coquereli|Chrysemys_picta_bellii|Pelusios_castaneus|Dicentrarchus_labrax|Malurus_cyaneus_samueli|Sus_scrofa_meishan|Sphenodon_punctatus|Mus_musculus_CAST_EiJ|Salmo_salar_north_american_atlantic_salmon|Procavia_capensis|Rattus_norvegicus_SHRSPBbbUtx|Gasterosteus_aculeatus|Pygocentrus_nattereri|Cyprinodon_variegatus|Sus_scrofa_rongchang|Ciona_savignyi|Physeter_catodon|Chlorocebus_sabaeus|Haplochromis_burtoni|Cavia_aperea|Oryctolagus_cuniculus|Periophthalmus_magnuspinnatus|Saccharomyces_cerevisiae|Peromyscus_maniculatus_bairdii|Echeneis_naucrates|Mandrillus_leucophaeus|Sus_scrofa_ossabaw_miniature|Drosophila_melanogaster|Oryzias_latipes_hni|Ovis_aries_kermani|Amazona_collaria|Delphinapterus_leucas|Calidris_pygmaea|Geospiza_fortis|Spermophilus_dauricus|Gallus_gallus_GCA_000002315.5|Ornithorhynchus_anatinus|Mus_caroli|Myotis_lucifugus|Phascolarctos_cinereus|Salmo_trutta|Bos_grunniens|Macaca_fascicularis|Pongo_abelii|Maylandia_zebra|Ovis_aries_rambouillet|Anser_brachyrhynchus|Latimeria_chalumnae|Serinus_canaria|Mesocricetus_auratus|Gallus_gallus|Stegastes_partitus|Panthera_pardus|Oreochromis_aureus|Neogobius_melanostomus|Oryzias_javanicus|Gadus_morhua|Anolis_carolinensis|Mus_musculus_PWK_PhJ|Ficedula_albicollis|Urocitellus_parryii|Notamacropus_eugenii|Sus_scrofa_nihs_2020|Echinops_telfairi|Mola_mola|Mus_musculus_LP_J|Catharus_ustulatus|Pavo_cristatus|Strix_occidentalis_caurina|Sciurus_vulgaris|Gopherus_agassizii|Cairina_moschata_domestica|Manacus_vitellinus|Oryzias_sinensis|Cebus_imitator|Eptatretus_burgeri|Anas_platyrhynchos|Poecilia_mexicana|Struthio_camelus_australis|Erpetoichthys_calabaricus|Paramormyrops_kingsleyae|Sinocyclocheilus_grahami|Seriola_lalandi_dorsalis|Mus_musculus_C3H_HeJ|Rattus_norvegicus_WKYBbb|Sus_scrofa_berkshire|Meriones_unguiculatus|Monodelphis_domestica|Rhinolophus_ferrumequinum|Callorhinchus_milii|Clupea_harengus|Cyprinus_carpio_german_mirror|Taeniopygia_guttata|Mus_musculus_CBA_J|Xenopus_tropicalis|Capra_hircus_blackbengal|Crocodylus_porosus|Salmo_salar_north_american_origin_brian|Sus_scrofa_euw1|Seriola_dumerili|Neolamprologus_brichardi|Esox_lucius|Cricetulus_griseus_chok1gshd|Microtus_ochrogaster|Tursiops_truncatus|Salmo_salar|Sus_scrofa_landrace|Athene_cunicularia|Larimichthys_crocea|Canis_lupus_familiarisgermanshepherd|Sus_scrofa|Mastacembelus_armatus|Otolemur_garnettii|Poecilia_formosa|Melopsittacus_undulatus|Heterocephalus_glaber_male|Nannospalax_galili|Cricetulus_griseus_picr|Astyanax_mexicanus_pachon|Cyclopterus_lumpus|Sus_scrofa_largewhite|Parus_major|Lepidothrix_coronata|Betta_splendens|Hucho_hucho|Vicugna_pacos|Cricetulus_griseus_crigri|Petromyzon_marinus|Oncorhynchus_tshawytscha|Aotus_nancymaae|Sparus_aurata|Xiphophorus_couchianus|Chinchilla_lanigera|Leptobrachium_leishanense|Bubo_bubo|Lonchura_striata_domestica|Mus_spicilegus|Mus_musculus_BALB_cJ|Ictalurus_punctatus|Canis_lupus_dingo|Homo_sapiens|Varanus_komodoensis|Junco_hyemalis|Mus_pahari|Notechis_scutatus|Bos_indicus_hybrid|Phasianus_colchicus|Ciona_intestinalis|Rhinopithecus_bieti|Oryzias_melastigma|Microcebus_murinus|Acanthochromis_polyacanthus|Theropithecus_gelada|Salarias_fasciatus|Dipodomys_ordii|Oncorhynchus_kisutch|Gasterosteus_aculeatus_freshwater_bot|Sus_scrofa_bama_miniature|Dromaius_novaehollandiae|Cynoglossus_semilaevis|Ovis_aries_romanov|Gadus_morhua_celtic_sea|Sarcophilus_harrisii|Ovis_aries_qiaoke|Cercocebus_atys|Heterocephalus_glaber_female|Falco_tinnunculus|Phocoena_sinus|Poecilia_reticulata|Zonotrichia_albicollis|Cavia_porcellus|Otus_sunia|Pan_paniscus|Pteropus_vampyrus|Canis_lupus_familiaris|Sus_scrofa_ningxiang|Sphaeramia_orbicularis|Stachyris_ruficeps|Scleropages_formosus|Numida_meleagris|Catagonus_wagneri|Salvator_merianae|Corvus_moneduloides|Ursus_americanus|Nothobranchius_furzeri|Lates_calcarifer|Mus_musculus|Rattus_norvegicus_SHRUtx|Neovison_vison|Cyprinus_carpio_hebao_red|Tupaia_belangeri|Danio_rerio|Panthera_leo|Oncorhynchus_mykiss|Coturnix_japonica|Ursus_maritimus|Sus_scrofa_tibetan|Balaenoptera_musculus|Apteryx_haastii|Dasypus_novemcinctus|Sus_scrofa_meishan_GCA_017957985.1|Kryptolebias_marmoratus|Bos_mutus|Mustela_putorius_furo|Capra_hircus_xinong_saanen_dairy|Felis_catus|Oryzias_latipes_hsok|Denticeps_clupeoides|Loxodonta_africana|Erinaceus_europaeus|Gopherus_evgoodei|Parambassis_ranga|Oreochromis_niloticus|Amphiprion_ocellaris|Amphiprion_percula|Electrophorus_electricus|Cervus_hanglu_yarkandensis|Monopterus_albus|Sus_scrofa_duroc|Chelonoidis_abingdonii|Astyanax_mexicanus|Zosterops_lateralis_melanops|Myripristis_murdjan|Equus_asinus|Cyprinus_carpio_huanghe|Sander_lucioperca|Salmo_salar_european_origin_alta|Choloepus_hoffmanni|Cyprinus_carpio_carpio|Pelodiscus_sinensis|Strigops_habroptila|Piliocolobus_tephrosceles|Ovis_aries_polled_dorset|Anabas_testudineus|Nothoprocta_perdicaria|Gallus_gallus_GCA_016700215.2|Panthera_tigris_altaica|P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