biopipen 0.7.1__py3-none-any.whl → 0.8.0__py3-none-any.whl

biopipen/ns/tcr.py

@@ -116,7 +116,6 @@ class ImmunarchFilter(Proc):
             Placeholders like `{Sample}_` can be used to from the meta data
         metacols: The extra columns to be exported to the group file.
     """
-
     input = "immdata:file, filterfile:file"
     output = """
         outfile:file:{{in.immdata | stem}}.RDS,
@@ -209,7 +208,6 @@ class Immunarch(Proc):
             If you do want multiple parameter sets for the same K, You can use
             a float number as the K. For example: `5.1` for K `5`.
     """
-
     input = "immdata:file"
     output = "outdir:dir:{{in.immdata | stem}}.immunarch"
     lang = config.lang.rscript
@@ -341,7 +339,6 @@ class CloneResidency(Proc):
         sample_groups: How the samples aligned in the report.
             Useful for cohort with large number of samples.
     """
-
     input = "immdata:file"
     output = "outdir:dir:{{in.immdata | stem}}.cloneov"
     lang = config.lang.rscript
@@ -366,7 +363,6 @@ class Immunarch2VDJtools(Proc):
         outdir: The output directory containing the vdjtools input for each
             sample
     """
-
     input = "immdata:file"
     output = "outdir:dir:{{in.immdata | stem}}.vdjtools_input"
     lang = config.lang.rscript
@@ -451,7 +447,6 @@ class Attach2Seurat(Proc):
             `{Sample}_` to use the meta data from the immunarch object
         metacols: Which meta columns to attach
     """
-
     input = "immfile:file, sobjfile:file"
     output = "outfile:file:{{in.sobjfile | basename}}"
     lang = config.lang.rscript
@@ -505,12 +500,10 @@ class TCRClustering(Proc):
             For ClusTCR, they will be passed to `clustcr.Clustering(...)`
 
     Requires:
-        - name: clusTCR
-          if: {{ proc.envs.tool == 'ClusTCR' }}
-          check: |
-            {{ proc.envs.python }} -c "import clustcr"
+        clusTCR:
+            - if: {{ proc.envs.tool == 'ClusTCR' }}
+            - check: {{ proc.envs.python }} -c "import clustcr"
     """
-
     input = "immfile:file"
     output = [
         "immfile:file:{{in.immfile | basename}}",
@@ -549,11 +542,9 @@ class TCRClusteringStats(Proc):
             the diversities by groups
 
     Requires:
-        - name: r-immunarch
-          check: |
-            {{proc.lang}} -e "library(immunarch)"
+        r-immunarch:
+            - check: {{proc.lang}} -e "library(immunarch)"
     """
-
     input = "immfile:file"
     output = "outdir:dir:{{in.immfile | stem}}.tcrclusters_stats"
     lang = config.lang.rscript
@@ -602,7 +593,6 @@ class CloneSizeQQPlot(Proc):
         on: The key of the metadata to use for the QQ plot. One/Both of
             `["Clones", "Proportion"]`
     """
-
     input = "immdata:file"
     output = "outdir:dir:{{in.immdata | stem}}.qqplots"
     lang = config.lang.rscript

biopipen/ns/vcf.py

@@ -18,7 +18,6 @@ class VcfLiftOver(Proc):
         tmpdir: Directory for temporary storage of working files
         args: Other CLI arguments for `gatk LiftoverVcf`
     """
-
     input = "invcf:file"
     output = "outvcf:file:{{in.invcf | basename}}"
     envs = {
@@ -61,7 +60,6 @@ class VcfFilter(Proc):
         helper: Some helper code for the filters
         keep: Keep the variants not passing the filters?
     """  # noqa: E501
-
     input = "invcf:file"
     output = "outfile:file:{{in.invcf | basename}}"
     lang = config.lang.python
@@ -87,7 +85,6 @@ class VcfIndex(Proc):
     Envs:
         tabix: Path to tabix
     """
-
     input = "infile:file"
     output = """
         {%- if in.infile.endswith(".gz") %}
@@ -120,11 +117,9 @@ class Vcf2Bed(Proc):
         outbase: The coordinate base of the base file
 
     Requires:
-        - name: cyvcf2
-          check: |
-            {{proc.lang}} -c "import cyvcf2"
+        cyvcf2:
+            - check: {{proc.lang}} -c "import cyvcf2"
     """
-
     input = "infile:file"
     output = "outfile:file:{{in.infile | stem0}}.bed"
     lang = config.lang.python
@@ -147,10 +142,10 @@ class VcfDownSample(Proc):
             If `n > 1`, it is the number.
             If `n <= 1`, it is the fraction.
     """
-
     input = "infile:file"
     output = "outfile:file:{{in.infile | basename}}"
     envs = {"n": 0}
+    lang = config.lang.bash
     script = "file://../scripts/vcf/VcfDownSample.sh"
 
 
@@ -290,14 +285,7 @@ class VcfFix(Proc):
         helpers: raw code the provide some helpers for the fixes
             The code will automatically dedented if given as a string. A list
             of strings is also supported and will be joined with newlines.
-
-    Requires:
-        - name: biopipen
-          check: |
-            {{proc.lang}} -c "import biopipen"
-
     """
-
     input = "infile:file"
     output = "outfile:file:{{in.infile | basename}}"
     lang = config.lang.python
@@ -305,6 +293,44 @@ class VcfFix(Proc):
     script = "file://../scripts/vcf/VcfFix.py"
 
 
+class VcfAnno(Proc):
+    """Annotate a VCF file using vcfanno
+
+    https://github.com/brentp/vcfanno
+
+    Input:
+        infile: The input VCF file
+        conffile: The configuration file for vcfanno or configuration dict
+            itself
+
+    Output:
+        outfile: The output VCF file
+
+    Envs:
+        vcfanno: Path to vcfanno
+        ncores: Number of cores to use
+        conffile: configuration file for vcfanno or configuration dict itself
+            This is ignored when `conffile` is given as input
+        args: Additional arguments to pass to vcfanno
+
+    Requires:
+        - name: vcfanno
+          check: |
+            {{proc.envs.vcfanno}} --help
+    """
+
+    input = "infile:file, conffile"
+    output = "outfile:file:{{in.infile | stem0}}.{{envs.tool}}.vcf"
+    lang = config.lang.python
+    envs = {
+        "vcfanno": config.exe.vcfanno,
+        "ncores": config.misc.ncores,
+        "conffile": {},
+        "args": {"permissive-overlap": True},
+    }
+    script = "file://../scripts/vcf/VcfAnno.py"
+
+
 class TruvariBench(Proc):
     """Run `truvari bench` to compare a VCF with CNV calls and
     base CNV standards
@@ -323,11 +349,9 @@ class TruvariBench(Proc):
         `<other>`: Ohter `truvari bench` arguments
 
     Requires:
-        - name: truvari
-          check: |
-            {{proc.envs.truvari}} version
+        truvari:
+            - check: {{proc.envs.truvari}} version
     """
-
     input = "compvcf:file, basevcf:file"
     output = "outdir:dir:{{in.compvcf | stem0 | append: '.truvari_bench'}}"
     envs = {
@@ -340,6 +364,7 @@ class TruvariBench(Proc):
         "typeignore": False,
         "multimatch": False,
     }
+    lang = config.lang.bash
     script = "file://../scripts/vcf/TruvariBench.sh"
 
 
@@ -363,21 +388,15 @@ class TruvariBenchSummary(Proc):
         devpars: The parameters to use for the plots.
 
     Requires:
-        - name: r-ggprism
-          check: |
-            {{proc.lang}} -e "library(ggprism)"
-        - name: r-rjson
-          check: |
-            {{proc.lang}} -e "library(rjson)"
-        - name: r-dplyr
-          check: |
-            {{proc.lang}} -e "library(dplyr)"
-        - name: r-ggplot2
-          check: |
-            {{proc.lang}} -e "library(ggplot2)"
-
+        r-ggprism:
+            - check: {{proc.lang}} -e "library(ggprism)"
+        r-rjson:
+            - check: {{proc.lang}} -e "library(rjson)"
+        r-dplyr:
+            - check: {{proc.lang}} -e "library(dplyr)"
+        r-ggplot2:
+            - check: {{proc.lang}} -e "library(ggplot2)"
     """
-
     input = "indirs:files"
     input_data = lambda ch: [list(ch.iloc[:, 0])]
     output = "outdir:dir:truvari_bench.summary"
@@ -411,7 +430,6 @@ class TruvariConsistency(Proc):
             annotations will be added as row annotations.
             Other options see also `biopipen.ns.plot.Heatmap`.
     """
-
     input = "vcfs:files"
     output = (
         "outdir:dir:"

biopipen/ns/web.py

@@ -1,5 +1,4 @@
 """Get data from the web"""
-
 from ..core.proc import Proc
 from ..core.config import config
 
@@ -22,16 +21,11 @@ class Download(Proc):
         ncores: The number of cores to use
 
     Requires:
-        - name: wget
-          message: Only required when envs.tool == "wget"
-          check: |
-            {{proc.envs.wget}} --version
-        - name: aria2c
-          message: Only required when envs.tool == "aria2c"
-          check: |
-            {{proc.envs.aria2c}} --version
+        wget: Only required when envs.tool == "wget"
+            - check: {{proc.envs.wget}} --version
+        aria2c: Only required when envs.tool == "aria2c"
+            - check: {{proc.envs.aria2c}} --version
     """
-
     input = "url"
     output = (
         "outfile:file:"
@@ -66,16 +60,11 @@ class DownloadList(Proc):
         ncores: The number of cores to use
 
     Requires:
-        - name: wget
-          message: Only required when envs.tool == "wget"
-          check: |
-            {{proc.envs.wget}} --version
-        - name: aria2c
-          message: Only required when envs.tool == "aria2c"
-          check: |
-            {{proc.envs.aria2c}} --version
+        wget: Only required when envs.tool == "wget"
+            - check: {{proc.envs.wget}} --version
+        aria2c: Only required when envs.tool == "aria2c"
+            - check: {{proc.envs.aria2c}} --version
     """
-
     input = "urlfile:file"
     output = "outdir:dir:{{in.urlfile | stem}}.downloaded"
     lang = config.lang.python

biopipen/reports/bam/CNAClinic.svelte

@@ -1,5 +1,5 @@
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 {% for gwpng in job.out.outdir | glob: "*/*.png" %}

biopipen/reports/bam/CNVpytor.svelte

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import table_of_images -%}
 <script>
-    import { Image } from "@@";
-    import { Tabs, Tab, TabContent } from "carbon-components-svelte";
+    import { Image } from "$lib";
+    import { Tabs, Tab, TabContent } from "$ccs";
 </script>
 
 {% for case in envs.cases %}

biopipen/reports/bam/ControlFREEC.svelte

@@ -1,6 +1,6 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 <script>
-    import { Image, DataTable } from "@@";
+    import { Image, DataTable } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/cnv/AneuploidyScore.svelte

@@ -1,8 +1,8 @@
 {% from "utils/misc.liq" import report_jobs -%}
 
 <script>
-    import { Image, DataTable } from "@@";
-    import { Tabs, Tab, TabContent, Tile } from "carbon-components-svelte";
+    import { Image, DataTable } from "$lib";
+    import { Tabs, Tab, TabContent, Tile } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/cnv/AneuploidyScoreSummary.svelte

@@ -1,5 +1,5 @@
 <script>
-    import { Image, DataTable } from "@@";
+    import { Image, DataTable } from "$lib";
 </script>
 
 <h1>Total number of arm-level gains/losses</h1>

biopipen/reports/cnvkit/CNVkitDiagram.svelte

@@ -1,6 +1,6 @@
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/cnvkit/CNVkitHeatmap.svelte

@@ -1,6 +1,6 @@
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/cnvkit/CNVkitScatter.svelte

@@ -1,6 +1,6 @@
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/gsea/FGSEA.svelte

@@ -1,7 +1,7 @@
 {% from "utils/gsea.liq" import fgsea_report -%}
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image, DataTable } from "@@";
+    import { Image, DataTable } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/gsea/GSEA.svelte

@@ -1,8 +1,8 @@
 {% from "utils/misc.liq" import report_jobs -%}
 {% from "utils/gsea.liq" import gsea_report -%}
 <script>
-    import { Image, DataTable } from "@@";
-    import { Tile } from "carbon-components-svelte";
+    import { Image, DataTable } from "$lib";
+    import { Tile } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/scrna/CellsDistribution.svelte

@@ -1,6 +1,6 @@
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/scrna/DimPlots.svelte

@@ -1,6 +1,6 @@
 {% from "utils/misc.liq" import table_of_images, report_jobs -%}
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/scrna/GeneExpressionInvistigation.svelte

@@ -2,7 +2,7 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/scrna/MarkersFinder.svelte

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image, DataTable } from "@@";
-    import { Tabs, Tab, TabContent, InlineNotification } from "carbon-components-svelte";
+    import { Image, DataTable } from "$lib";
+    import { Tabs, Tab, TabContent, InlineNotification } from "$ccs";
 </script>
 
 

biopipen/reports/scrna/ScFGSEA.svelte

@@ -1,7 +1,7 @@
 {% from "utils/gsea.liq" import fgsea_report -%}
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image, DataTable } from "@@";
+    import { Image, DataTable } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/scrna/SeuratClusterStats.svelte

@@ -1,8 +1,8 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 {% from_ os import path %}
 <script>
-    import { DataTable, Image } from "@@";
-    import { Tabs, Tab, TabContent } from "carbon-components-svelte";
+    import { DataTable, Image } from "$lib";
+    import { Tabs, Tab, TabContent } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/scrna/SeuratPreparing.svelte

@@ -1,8 +1,8 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 {% from_ os import path %}
 <script>
-    import { Image } from "@@";
-    import { Tile } from "carbon-components-svelte";
+    import { Image } from "$lib";
+    import { Tile } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubsets.svelte

@@ -2,7 +2,7 @@
 {% from "utils/gsea.liq" import fgsea_report, gsea_report -%}
 
 <script>
-  import { Image, DataTable } from "@@";
+  import { Image, DataTable } from "$lib";
 </script>
 
 {%- macro report_job(job, h=2) -%}

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import report_jobs -%}
 
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 <h1>Introduction</h1>

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 {%- macro report_job(job, h=2) -%}

biopipen/reports/tcr/CloneResidency.svelte

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 <script>
-    import { Image, DataTable } from "@@";
-    import { Dropdown } from "carbon-components-svelte";
+    import { Image, DataTable } from "$lib";
+    import { Dropdown } from "$ccs";
 
     let count_sample;
 

biopipen/reports/tcr/Immunarch.svelte

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 <script>
-    import { Image } from "@@";
-    import { Tabs, Tab, TabContent, Tile, UnorderedList, p } from "carbon-components-svelte";
+    import { Image } from "$lib";
+    import { Tabs, Tab, TabContent, Tile, UnorderedList, p } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/tcr/SampleDiversity.svelte

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 <script>
-    import { Image } from "@@";
-    import { Tile } from "carbon-components-svelte";
+    import { Image } from "$lib";
+    import { Tile } from "$ccs";
 </script>
 
 

biopipen/reports/tcr/TCRClusteringStats.svelte

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image, DataTable } from "@@";
-    import { Tabs, Tab, TabContent } from "carbon-components-svelte";
+    import { Image, DataTable } from "$lib";
+    import { Tabs, Tab, TabContent } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/tcr/VJUsage.svelte

@@ -1,6 +1,6 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 <script>
-    import { Image } from "@@";
+    import { Image } from "$lib";
 </script>
 
 <h1>V-J usage plots</h1>

biopipen/reports/utils/gsea.liq

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import table_of_images -%}
 
 {%- macro fgsea_report_script() -%}
-import { Image, DataTable } from "../components";
+import { Image, DataTable } from "$lib";
 {%- endmacro -%}
 
 {%- macro fgsea_report(fgsea_dir, h, envs, nrows=100) -%}

biopipen/reports/utils/misc.liq

@@ -16,7 +16,7 @@
 
 
 {%- macro table_of_images_script() -%}
-import { Image } from "../components";
+import { Image } from "$lib";
 {%- endmacro -%}
 
 {%- macro table_of_images(srcs, caps=None, col=2, table_width=100) -%}

biopipen/reports/vcf/TruvariBenchSummary.svelte

@@ -1,6 +1,6 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 <script>
-    import { DataTable, Image } from "@@";
+    import { DataTable, Image } from "$lib";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/reports/vcf/TruvariConsistency.svelte

@@ -1,7 +1,7 @@
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image } from "@@";
-    import { Tile } from "carbon-components-svelte";
+    import { Image } from "$lib";
+    import { Tile } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/scripts/tcgamaf/maf2vcf.pl

@@ -6,6 +6,7 @@
 # https://github.com/mskcc/vcf2maf
 # This is modified to:
 # - Add path to samtools to arguments
+# - Add Variant_Classification and Variant_Type to INFO field
 # - Fix https://github.com/mskcc/vcf2maf/issues/234
 # - Adding logs
 
@@ -189,6 +190,8 @@ while( my $line = $maf_fh->getline ) {
                 $tn_vcf{$vcf_file} .= "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n";
                 $tn_vcf{$vcf_file} .= "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths of REF and ALT(s) in the order listed\">\n";
                 $tn_vcf{$vcf_file} .= "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth across this site\">\n";
+                $tn_vcf{$vcf_file} .= "##INFO=<ID=VC,Number=1,Type=String,Description=\"Variant_Classification\">\n";
+                $tn_vcf{$vcf_file} .= "##INFO=<ID=VT,Number=1,Type=String,Description=\"Variant_Type\">\n";
                 $tn_vcf{$vcf_file} .= "##FILTER=<ID=$_,Description=\"$_\">\n" foreach ( sort keys %filter_tags );
                 $tn_vcf{$vcf_file} .= "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t$t_id\t$n_id\n";
             }
@@ -203,7 +206,7 @@ while( my $line = $maf_fh->getline ) {
     }
 
     # For each variant in the MAF, parse out data that can go into the output VCF
-    my ( $chr, $pos, $ref, $al1, $al2, $t_id, $n_id, $n_al1, $n_al2, $id, $qual, $filter ) = map{ my $c = lc; ( defined $col_idx{$c} ? $cols[$col_idx{$c}] : "" )} qw( Chromosome Start_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 variant_id variant_qual FILTER );
+    my ( $chr, $pos, $ref, $al1, $al2, $t_id, $n_id, $n_al1, $n_al2, $id, $qual, $filter, $vc, $vt ) = map{ my $c = lc; ( defined $col_idx{$c} ? $cols[$col_idx{$c}] : "" )} qw( Chromosome Start_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 variant_id variant_qual FILTER Variant_Classification Variant_Type );
     $filter =~ s/,/;/g;
     ++$line_count;
 
@@ -321,12 +324,12 @@ while( my $line = $maf_fh->getline ) {
     # Contruct a VCF formatted line and append it to the respective VCF
     if( $per_tn_vcfs ) {
         my $vcf_file = "$output_dir/$t_id\_vs_$n_id.vcf";
-        my $vcf_line = join( "\t", $chr, $pos, $id, $ref, $alt, $qual, $filter, ".", "GT:AD:DP", $t_fmt, $n_fmt );
+        my $vcf_line = join( "\t", $chr, $pos, $id, $ref, $alt, $qual, $filter, "VC=$vc:VT=$vt", "GT:AD:DP", $t_fmt, $n_fmt );
         $tn_vcf{$vcf_file} .= "$vcf_line\n";
     }
 
     # Store VCF formatted data for the multi-sample VCF
-    my $key = join( "\t", $chr, $pos, $ref, $alt );
+    my $key = join( "\t", $chr, $pos, $ref, $alt, $vc, $vt );
     push( @var_key, $key ) unless( exists $var_frmt{ $key } );
     $var_frmt{ $key }{ $vcf_col_idx{ $t_id }} = $t_fmt;
     $var_frmt{ $key }{ $vcf_col_idx{ $n_id }} = $n_fmt;
@@ -356,14 +359,16 @@ $vcf_fh->print( $ref_header );
 $vcf_fh->print( "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n" );
 $vcf_fh->print( "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic Depths of REF and ALT(s) in the order listed\">\n" );
 $vcf_fh->print( "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\n" );
+$vcf_fh->print( "##INFO=<ID=VC,Number=1,Type=String,Description=\"Variant_Classification\">\n" );
+$vcf_fh->print( "##INFO=<ID=VT,Number=1,Type=String,Description=\"Variant_Type\">\n" );
 $vcf_fh->print( "##FILTER=<ID=$_,Description=\"$_\">\n" ) foreach ( sort keys %filter_tags );
 $vcf_fh->print( "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" . join("\t", @vcf_cols) . "\n" );
 
 # Write each variant into the multi-sample VCF
 print STDOUT "INFO: Writing multi-sample VCF\n";
 foreach my $key ( @var_key ) {
-    my ( $chr, $pos, $ref, $alt ) = split( "\t", $key );
-    $vcf_fh->print( join( "\t", $chr, $pos, $var_id{ $key }, $ref, $alt, $var_qual{ $key }, $var_fltr{ $key }, ".", "GT:AD:DP" ));
+    my ( $chr, $pos, $ref, $alt, $vc, $vt ) = split( "\t", $key );
+    $vcf_fh->print( join( "\t", $chr, $pos, $var_id{ $key }, $ref, $alt, $var_qual{ $key }, $var_fltr{ $key }, "VC=$vc;VT=$vt", "GT:AD:DP" ));
     map{ $vcf_fh->print( "\t" . (( exists $var_frmt{$key}{$_} ) ? $var_frmt{$key}{$_} : './.:.:.' ))}( 0..$#vcf_cols );
     $vcf_fh->print( "\n" );
 }