#@UGENE_WORKFLOW
#Call variants for an input assembly and a reference sequence using SAMtools mpileup and bcftool.
#Predict effects of the found variants using SnpEff.
workflow "Variant calling and effects prediction"{
read-assembly {
type:get-file-list;
name:"Read Assembly (BAM/SAM)";
url-in {
dataset:Dataset;
}
}
read-sequence {
type:get-file-list;
name:"Read Sequence";
url-in {
dataset:Dataset;
}
}
call_variants {
type:call_variants;
name:"Call Variants";
max-dep:100;
reference-source:port;
variants-url:variants.vcf;
}
files-conversion-1 {
type:files-conversion;
name:"To FASTA";
document-format:fasta;
}
files-conversion-2 {
type:files-conversion;
name:"To BAM";
document-format:bam;
}
rename-chromosome-in-variation {
type:rename-chromosome-in-variation;
name:"Chr Notation";
prefix-replace-with:chr;
prefixes-to-replace:"NC_00000;NC_0000";
}
seff {
type:seff;
name:"Annotate and Predict Effects with SnpEff";
}
convert-snpeff-variations-to-annotations {
type:convert-snpeff-variations-to-annotations;
name:"To Annotations";
}
.actor-bindings {
call_variants.out-variations->rename-chromosome-in-variation.in-file
files-conversion-2.out-file->call_variants.in-assembly
read-sequence.out-url->files-conversion-1.in-file
files-conversion-1.out-file->call_variants.in-sequence
seff.out-file->convert-snpeff-variations-to-annotations.in-variations-url
read-assembly.out-url->files-conversion-2.in-file
rename-chromosome-in-variation.out-file->seff.in-file
}
read-assembly.dataset->call_variants.in-assembly.dataset
files-conversion-2.url->call_variants.in-assembly.url
files-conversion-1.url->call_variants.in-sequence.url
read-sequence.url->files-conversion-1.in-file.url
read-assembly.url->files-conversion-2.in-file.url
call_variants.url->rename-chromosome-in-variation.in-file.url
rename-chromosome-in-variation.url->seff.in-file.url
seff.url->convert-snpeff-variations-to-annotations.in-variations-url.url
.meta {
parameter-aliases {
read-assembly.url-in {
alias:assembly_in;
}
read-sequence.url-in {
alias:seq_in;
}
call_variants.acgt_only {
alias:a_c_g_t;
}
call_variants.bcf_bed {
alias:bcf_bed;
}
call_variants.bed {
alias:bed_pos_list_file;
}
call_variants.disable_baq {
alias:BAQ;
}
call_variants.keepalt {
alias:retain_all_pos_alt;
}
call_variants.max_depth {
alias:max_reads_num;
}
call_variants.no_indel {
alias:no_indels;
}
call_variants.ptype {
alias:allele_freq_spect;
}
call_variants.theta {
alias:theta;
}
call_variants.variants-url {
alias:out_file;
}
}
visual {
call_variants {
pos:"-465 -510";
style:ext;
bg-color-ext:"0 129 94 64";
bounds:"-30 -30 123.125 72";
in-assembly.angle:176.73;
in-sequence.angle:235.098;
out-variations.angle:351.674;
}
convert-snpeff-variations-to-annotations {
pos:"-450 -285";
style:simple;
bg-color-simple:"234 223 240 255";
in-variations-url.angle:3.25195;
}
files-conversion-1 {
pos:"-615 -450";
style:simple;
bg-color-simple:"84 84 84 255";
in-file.angle:196.858;
out-file.angle:6.5198;
}
files-conversion-2 {
pos:"-615 -555";
style:simple;
bg-color-simple:"84 84 84 255";
in-file.angle:170.538;
out-file.angle:334.799;
}
read-assembly {
pos:"-870 -600";
style:ext;
bg-color-ext:"24 102 175 64";
bounds:"-30 -30 111.375 66";
out-url.angle:360;
}
read-sequence {
pos:"-885 -435";
style:ext;
bg-color-ext:"24 102 175 64";
bounds:"-30 -30 110.25 62";
out-url.angle:349.061;
}
rename-chromosome-in-variation {
pos:"-210 -495";
style:simple;
bg-color-simple:"232 227 230 255";
in-file.angle:180;
out-file.angle:270.785;
}
seff {
pos:"-270 -285";
style:ext;
bg-color-ext:"0 129 94 64";
in-file.angle:28.6105;
out-file.angle:181.848;
}
call_variants.out-variations->rename-chromosome-in-variation.in-file {
text-pos:"-45 -43";
}
files-conversion-1.out-file->call_variants.in-sequence {
text-pos:"-19 -31";
}
files-conversion-2.out-file->call_variants.in-assembly {
text-pos:"-12 -24";
}
read-assembly.out-url->files-conversion-2.in-file {
text-pos:"-37 -11";
}
read-sequence.out-url->files-conversion-1.in-file {
text-pos:"-31 -21";
}
rename-chromosome-in-variation.out-file->seff.in-file {
text-pos:"-45 -43";
}
seff.out-file->convert-snpeff-variations-to-annotations.in-variations-url {
text-pos:"-45 -43";
}
}
wizard {
auto-run: true;
name:"Call Variants Wizard";
page {
id:1;
next:2;
title:"Input reference sequence and assembly";
parameters-area {
group {
title:"Input files";
lineedit-and-dataset {
read-sequence.url-in {
label:"Reference sequence file";
}
read-assembly.url-in {
label:"BAM/SAM file";
}
}
}
}
}
page {
id:2;
next:3;
title:"SAMtools mpileup parameters";
parameters-area {
group {
title:Parameters;
label-size:200;
call_variants.use_orphan {
}
call_variants.disable_baq {
}
call_variants.capq_thres {
}
call_variants.max_depth {
}
call_variants.ext_baq {
}
call_variants.bed {
}
call_variants.reg {
}
call_variants.min_mq {
}
call_variants.min_baseq {
}
}
group {
title:Additional;
label-size:200;
type:hideable;
call_variants.illumina13-encoding {
}
call_variants.extQ {
}
call_variants.tandemQ {
}
call_variants.no_indel {
}
call_variants.max_indel_depth {
}
call_variants.openQ {
}
call_variants.pl_list {
}
}
}
}
page {
id:3;
next:4;
title:"SAMtools bcftools view parameters";
parameters-area {
group {
title:Parameters;
label-size:200;
call_variants.keepalt {
}
call_variants.fix_pl {
}
call_variants.no_geno {
}
call_variants.acgt_only {
}
call_variants.bcf_bed {
}
call_variants.qcall {
}
call_variants.samples {
}
call_variants.min_smpl_frac {
}
call_variants.call_gt {
}
}
group {
title:Additional;
label-size:200;
type:hideable;
call_variants.indel_frac {
}
call_variants.pref {
}
call_variants.ptype {
}
call_variants.theta {
}
call_variants.ccall {
}
call_variants.n1 {
}
call_variants.n_perm {
}
call_variants.min_perm_p {
}
}
}
}
page {
id:4;
next:5;
title:"SAMtools vcfutils varFilter parameters";
parameters-area {
group {
title:Parameters;
label-size:200;
call_variants.print-filtered {
}
call_variants.min-qual {
}
call_variants.min-dep {
}
call_variants.max-dep {
}
call_variants.min-alt-bases {
}
call_variants.gap-size {
}
call_variants.window {
}
}
group {
title:Additional;
label-size:200;
type:hideable;
call_variants.min-strand {
}
call_variants.min-baseQ {
}
call_variants.min-mapQ {
}
call_variants.min-end-distance {
}
call_variants.min-hwe {
}
}
}
}
page {
id:5;
next:6;
title:"Change chromosome notation for variations";
parameters-area {
group {
title:Parameters;
label-size:150;
rename-chromosome-in-variation.prefixes-to-replace {
}
rename-chromosome-in-variation.prefix-replace-with {
}
}
}
}
page {
id:6;
next:7;
title:"SnpEff parameters";
parameters-area {
group {
title:Parameters;
label-size:200;
seff.genome {
}
}
group {
title:Additional;
label-size:200;
type:hideable;
seff.canon {
}
seff.hgvs {
}
seff.lof {
}
seff.motif {
}
seff.updown-length {
}
}
}
}
page {
id:7;
title:"Output files";
parameters-area {
group {
title:"Output variants";
label-size:110;
call_variants.variants-url {
label:"Output VCF file"
}
convert-snpeff-variations-to-annotations.url-out {
label:"Output GenBank file"
}
}
}
}
}
}
}