| Previous changeset 4:5c5cdbdc3534 (2018-12-14) Next changeset 6:b2c25142267e (2019-02-06) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 |
|
modified:
gemini_load.xml gemini_macros.xml repository_dependencies.xml test-data/gemini_amend_input.db test-data/gemini_annotate_result.db test-data/gemini_auto_dom_input.db test-data/gemini_auto_rec_input.db test-data/gemini_comphets_input.db test-data/gemini_de_novo_input.db test-data/gemini_is_somatic_result.db test-data/gemini_load_result1.db test-data/gemini_load_result2.db test-data/gemini_versioned_databases.loc test-data/test-cache/gemini-config.yaml |
|
added:
test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi |
|
removed:
test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca gemini_load.xml --- a/gemini_load.xml Fri Dec 14 13:01:22 2018 -0500 +++ b/gemini_load.xml Fri Jan 11 17:50:01 2019 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">\n+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">\n <description>Loading a VCF file into GEMINI</description>\n <macros>\n <import>gemini_macros.xml</import>\n@@ -11,7 +11,7 @@\n <![CDATA[\n @PROVIDE_ANNO_DATA@\n \n- ln -s "${ infile }" input.vcf &&\n+ ln -s \'$infile\' input.vcf &&\n bgzip -c input.vcf > input.vcf.gz &&\n tabix -p vcf input.vcf.gz &&\n \n@@ -19,62 +19,77 @@\n @BINARY@\n -v input.vcf.gz\n #if str( $annotation_type ) != "None":\n- -t "$annotation_type"\n+ -t $annotation_type\n #end if\n \n+ $has_genotypes\n+\n #if $ped:\n -p $ped\n #end if\n \n- $skip_gerp_bp\n- $skip_cadd\n- $skip_gene_tables\n- $no_load_genotypes\n- $no_genotypes\n- $passonly\n- $infostring\n+ #if \'gerp_bp\' not in str($opt_content):\n+ --skip-gerp-bp\n+ #end if\n+ #if \'cadd\' not in str($opt_content):\n+ --skip-cadd\n+ #end if\n+ #if \'gene_tables\' not in str($opt_content):\n+ --skip-gene-tables\n+ #end if\n+ #if \'genotypes\' not in str($opt_content):\n+ --no-load-genotypes\n+ #end if\n+ #if \'gt_pl\' not in str($opt_content):\n+ --skip-pls\n+ #end if\n+ #if \'passonly\' in str($opt_content):\n+ --passonly\n+ #end if\n+ #if \'info_string\' in str($opt_content):\n+ --save-info-string\n+ #end if\n+\n --cores \\${GALAXY_SLOTS:-4}\n \n- "${ outfile }"\n+ \'$outfile\'\n ]]>\n </command>\n <inputs>\n- <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported.">\n+ <param name="infile" type="data" format="vcf"\n+ label="VCF dataset to be loaded in the GEMINI database"\n+ help="Only build 37 (aka hg19) of the human genome is supported.">\n <options>\n <filter type="add_value" value="hg19" />\n <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />\n <filter type="add_value" value="hg_g1k_v37" />\n </options>\n </param>\n-\n- <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">\n- <option value="None">None (not recommended)</option>\n- <option value="snpEff" selected="True">snpEff annotated VCF file</option>\n- <option value="VEP">VEP annotated VCF file</option>\n+ <param argument="-t" name="annotation_type" type="select"\n+ label="The variants in this input are"\n+ help="GEMINI can parse and use annotations generated with either snpEff (both \'EFF\'- and \'ANN\'-style annotations are supported) or VEP. You can also load unannotated variants, but most of GEMINI\'s functionality will not be available or not be very useful without annotations.">\n+ <option value="snpEff" selected="True">annotated with snpEff</option>\n+ <option value="VEP">annotated with VEP</option>\n+ <option value="None">not annotated (not recommended)</option>\n </param>\n- <param name="ped" type="data" format="tabular" optional="True" label="Sample information file in PED+ format" help="(-p)" />\n+ <param argument="--no-genotypes" name="has_genotypes" type="boolean" falsevalue="--no-genotypes" truevalue="" checked="True"\n+ label="This input comes with genotype calls for its samples"\n+ help="This is usually the case, but some published datasets, like some 1000G VCFs, are missing genotype information."/>\n <expand mac'..b'fully leverage the power of GEMINI, you should first **annotate your VCF\n+dataset** with the functional consequences of the variants using either *VEP*\n+or *snpEff*.\n+\n+.. class:: Warning mark\n+\n+ To avoid problems during annotation, but also during later variant queries with\n+ GEMINI tools, it is good practice to preprocess your VCF dataset even before\n+ annoation to split records with multiple alternate alleles, and to left-align\n+ and trim indels. The authors of GEMINI recommend the tool *vt* for this purpose,\n+ an equivalently good option is *bcftools norm*, and Galaxy wrappers exist for\n+ both tools.\n+\n+In addition, you are encouraged to provide **family and sample phenotype\n+information in PED format**, if you are planning to use GEMINI for any kind of\n+variant identification based on inheritance patterns.\n+\n+A PED file is simply a tabular text file (columns can be separated by either\n+spaces or TABs, but not a mixture of the two within the same file) with the\n+header::\n+\n+ #family_id name paternal_id maternal_id sex phenotype\n+\n+and optional additional columns. The actual column names in the header are not\n+fixed, but there have to be at least six columns that are interpreted as\n+detailed next.\n+\n+Subsequent lines describe one sample from the VCF input dataset each, where\n+\n+- *family_id* is an alphanumeric identifier of a family\n+\n+ If the family, to which the sample belongs, is unknown, a placeholder of\n+ ``0``, ``-9`` or ``None`` can be used to indicate this fact.\n+\n+- *name* is the identifier of the sample described by the line\n+\n+- *paternal_id* is the identifier of the sample\'s father\n+\n+ If the sample\'s father is not available in the VCF, a placeholder of\n+ ``0``, ``-9`` or ``None`` can be used to indicate this fact.\n+\n+- *maternal_id* is the identifier of the sample\'s mother\n+\n+ If the sample\'s mother is not available in the VCF, a placeholder of\n+ ``0``, ``-9`` or ``None`` can be used to indicate this fact.\n+\n+- *sex* is a numeric code for the sample\'s sex\n+ (1=male, 2=female, any other number=unknown sex)\n+\n+- *phenotype* is a numeric code for the sample\'s phenotypic affection status\n+ (1=unaffected, 2=affected)\n+\n+ If the sample\'s phenotype is unknown, a placeholder of ``0`` or ``-9`` can be\n+ used to indicate this fact.\n+\n+- Optional additional columns can have any column name you like, and accept any\n+ per-sample value. The data from such extra columns will be added to the\n+ samples table of the GEMINI database so you can use them in queries. Extra\n+ columns can be used, *e.g.*, to describe additional phenotypes.\n+\n+- If no extra columns are present in a PED file, then the header line is\n+ optional.\n+\n+Here are two examples of valid PED file contents::\n+\n+ #family_id name paternal_id maternal_id sex phenotype hair_color\n+ 1 M10475 -9 -9 1 1 brown\n+ 1 M10478 M10475 M10500 2 2 brown\n+ 1 M10500 -9 -9 2 2 black\n+ 1 M128215 M10475 M10500 1 1 blue\n+\n+This describes a family with two kids, in which mother and daughter, but not\n+father and son are phenotypically affected. The file also stores the hair color\n+of all family members.\n+\n+::\n+\n+ #family_id name paternal_id maternal_id sex phenotype\n+ 0 M10475 0 0 -1 1\n+ 0 M10478 0 0 -1 2\n+ 0 M10500 0 0 -1 2\n+ 0 M128215 0 0 -1 1\n+\n+This describes the same samples as above, but without recording family\n+structure, sex or additional traits. Only the sample phenotypes are provided.\n+In this case (no extra columns), the header line could be omitted.\n \n ]]></help>\n <expand macro="citations"/>\n' |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca gemini_macros.xml --- a/gemini_macros.xml Fri Dec 14 13:01:22 2018 -0500 +++ b/gemini_macros.xml Fri Jan 11 17:50:01 2019 -0500 |
| [ |
| b'@@ -1,15 +1,12 @@\n <macros>\n <!-- gemini version to be used -->\n- <token name="@VERSION@">0.18.1</token>\n+ <token name="@VERSION@">0.20.1</token>\n <!-- minimal annotation files version required by this version of gemini -->\n- <token name="@DB_VERSION@">181</token>\n+ <token name="@DB_VERSION@">200</token>\n \n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@VERSION@">gemini</requirement>\n- <requirement type="package" version="0.2.6">tabix</requirement>\n- <!-- for conda useage -->\n- <!--requirement type="package" version="1.3.1">htslib</requirement-->\n <yield />\n </requirements>\n </xml>\n@@ -24,9 +21,17 @@\n <exit_code range=":-1" />\n <regex match="Error:" />\n <regex match="Exception:" />\n+ <yield />\n </stdio>\n </xml>\n \n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1371/journal.pcbi.1003153</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n <xml name="annotation_dir">\n <param name="annotation_databases" type="select" label="Choose a gemini annotation source">\n <options from_data_table="gemini_versioned_databases">\n@@ -36,31 +41,36 @@\n </param>\n </xml>\n \n- <xml name="add_header_column">\n- <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" \n- label="Add a header of column names to the output" help="(--header)"/>\n- </xml>\n-\n- <xml name="radius">\n- <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >\n- <validator type="in_range" min="0"/>\n+ <xml name="infile">\n+ <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >\n+ <options options_filter_attribute="metadata.gemini_version" >\n+ <filter type="add_value" value="@VERSION@" />\n+ </options>\n </param>\n </xml>\n- <xml name="variant_mode">\n- <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" \n- label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>\n+\n+ <xml name="add_header_column">\n+ <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True" \n+ label="Add a header of column names to the output" />\n </xml>\n \n- <xml name="column_filter">\n+ <xml name="column_filter" token_help="" token_minimalset="variant_id, gene">\n <conditional name="report">\n- <param name="report_selector" type="select" label="Columns to include in the report"\n- help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">\n- <option value="all" selected="True">all</option>\n- <option value="column_filter">User given columns</option>\n+ <param name="report_selector" type="select"\n+ label="Set of columns to include in the variant report table"\n+ help="@HELP@">\n+ <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option>\n+ <option value="full">Full (report all columns defined in the GEMINI database variants table)</option>\n+ <option value="custom">Custom (report user-specified columns)</option>\n </param>\n- <when value="all"/>\n- <when value="column_filter">\n- <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">\n+ <when value="full" />\n+ <when value="minimal">\n+ '..b'r($report.extra_cols).strip():\n+ #if $cols:\n+ #set $cols = $cols + \', \' + str($report.extra_cols)\n+ #else:\n+ #set $cols = str($report.extra_cols)\n+ #end if\n+ #end if\n+ #if not $cols:\n+ #set $cols = "variant_id, gene"\n+ #end if\n #end if\n </token>\n \n <token name="@COLUMN_SELECT@">\n- #if $report.report_selector != \'all\':\n- --columns "${report.columns}\n- #if str($report.extra_cols).strip()\n- #echo \',\'+\',\'.join(str($report.extra_cols).split()) \n- #end if\n- "\n+ @SET_COLS@\n+ #if $cols != "*"\n+ --columns \'$cols\'\n #end if\n </token>\n \n- <xml name="family">\n- <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>\n- </xml>\n-\n- <xml name="lenient">\n- <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/>\n- </xml>\n-\n- <xml name="unaffected">\n- <param name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False" label="Report candidates that also impact samples labeled as unaffected." help="(--allow-unaffected)"/>\n- </xml>\n-\n- <xml name="min_kindreds">\n- <param name="min_kindreds" type="integer" value="1" label="The min. number of kindreds that must have a candidate variant in a gene" help="default: 1 (--min-kindreds)" />\n- </xml>\n-\n- <xml name="min_sequence_depth">\n- <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"\n- help="default: 0 (-d)" />\n- </xml>\n-\n- <xml name="min_gq">\n- <param name="min_gq" type="integer" value="0" label="the minimum genotype quality required for each sample in a family" help="default: 0 (--min-gq)">\n- <validator type="in_range" min="0"/>\n- </param>\n- </xml>\n-\n- <xml name="gt_pl_max">\n- <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1371/journal.pcbi.1003153</citation>\n- <yield />\n- </citations>\n- </xml>\n-\n- <xml name="infile">\n- <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >\n- <options options_filter_attribute="metadata.gemini_version" >\n- <filter type="add_value" value="@VERSION@" />\n- </options>\n- <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator>\n- </param>\n- </xml>\n-\n+ <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[\n+ #set $region_elements = []\n+ #for $r in $regions:\n+ ## The actual chromosome name needs to be single-quoted\n+ ## in SQL, so we need to quote the single quotes like the\n+ ## sanitize_query macro would if the whole was a parameter.\n+ #set $r_elements = ["chrom = \'\\"\'\\"\'%s\'\\"\'\\"\'" % str($r.chrom).strip()]\n+ #if str($r.start).strip():\n+ #silent $r_elements.append("start >= %d" % int($r.start))\n+ #end if\n+ #if str($r.stop).strip():\n+ #silent $r_elements.append("end <= %d" % int($r.stop))\n+ #end if\n+ #silent $region_elements.append("(%s)" % " AND ".join($r_elements))\n+ #end for\n+ ]]>\n+ </token>\n </macros>\n' |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca repository_dependencies.xml --- a/repository_dependencies.xml Fri Dec 14 13:01:22 2018 -0500 +++ b/repository_dependencies.xml Fri Jan 11 17:50:01 2019 -0500 |
| b |
| @@ -1,4 +1,4 @@ <?xml version="1.0" ?> <repositories description="This requires the GEMINI data manager definition to install all required annotation databases."> - <repository changeset_revision="fe5a9a7d95b0" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository changeset_revision="f57426daa04d" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> </repositories> \ No newline at end of file |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_amend_input.db |
| b |
| Binary file test-data/gemini_amend_input.db has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_annotate_result.db |
| b |
| Binary file test-data/gemini_annotate_result.db has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_auto_dom_input.db |
| b |
| Binary file test-data/gemini_auto_dom_input.db has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_auto_rec_input.db |
| b |
| Binary file test-data/gemini_auto_rec_input.db has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_comphets_input.db |
| b |
| Binary file test-data/gemini_comphets_input.db has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_de_novo_input.db |
| b |
| Binary file test-data/gemini_de_novo_input.db has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_is_somatic_result.db |
| b |
| Binary file test-data/gemini_is_somatic_result.db has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_load_result1.db |
| b |
| Binary file test-data/gemini_load_result1.db has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_load_result2.db |
| b |
| Binary file test-data/gemini_load_result2.db has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/gemini_versioned_databases.loc --- a/test-data/gemini_versioned_databases.loc Fri Dec 14 13:01:22 2018 -0500 +++ b/test-data/gemini_versioned_databases.loc Fri Jan 11 17:50:01 2019 -0500 |
| b |
| @@ -1,3 +1,3 @@ ## GEMINI versioned databases #DownloadDate dbkey DBversion Description Path -1999-01-01 hg19 181 GEMINI annotations (test snapshot) ${__HERE__}/test-cache +1999-01-01 hg19 200 GEMINI annotations (test snapshot) ${__HERE__}/test-cache |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini-config.yaml --- a/test-data/test-cache/gemini-config.yaml Fri Dec 14 13:01:22 2018 -0500 +++ b/test-data/test-cache/gemini-config.yaml Fri Jan 11 17:50:01 2019 -0500 |
| b |
| @@ -2,12 +2,14 @@ versions: ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz: 4 ESP6500SI.all.snps_indels.tidy.v2.vcf.gz: 2 - ExAC.r0.3.sites.vep.tidy.vcf.gz: 3 + ExAC.r0.3.sites.vep.tidy.vcf.gz: 4 GRCh37-gms-mappability.vcf.gz: 2 - clinvar_20160203.tidy.vcf.gz: 5 + clinvar_20170130.tidy.vcf.gz: 5 cosmic-v68-GRCh37.tidy.vcf.gz: 3 - dbsnp.b141.20140813.hg19.tidy.vcf.gz: 4 + dbsnp.b147.20160601.tidy.vcf.gz: 1 detailed_gene_table_v75: 2 geno2mp.variants.tidy.vcf.gz: 1 + gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz: 2 hg19.rmsk.bed.gz: 2 summary_gene_table_v75: 2 + whole_genome_SNVs.tsv.compressed.gz: 2 |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz |
| b |
| Binary file test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi |
| b |
| Binary file test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz |
| b |
| Binary file test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi |
| b |
| Binary file test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz |
| b |
| Binary file test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi |
| b |
| Binary file test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz |
| b |
| Binary file test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi |
| b |
| Binary file test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz |
| b |
| Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz has changed |
| b |
| diff -r 5c5cdbdc3534 -r b5b53c27baca test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi |
| b |
| Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi has changed |