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changeset 3:65b400409455 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
author artbio
date Wed, 26 Aug 2020 12:24:07 -0400
parents 49a8a327cc72
children 49da975ba395
files lumpy_smoove.xml test-data/celegans_1.bam test-data/celegans_2.bam test-data/celegans_RG_1.bam test-data/celegans_RG_2.bam test-data/result-1.vcf test-data/result-2.vcf test-data/result-3.vcf test-data/result-4.vcf
diffstat 9 files changed, 160 insertions(+), 70 deletions(-) [+]
line wrap: on
line diff
--- a/lumpy_smoove.xml	Wed Aug 26 05:48:01 2020 -0400
+++ b/lumpy_smoove.xml	Wed Aug 26 12:24:07 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="lumpy_smoove" name="lumpy_smoove" version="0.4.0">
+<tool id="lumpy_smoove" name="lumpy_smoove" version="0.5.0">
     <description>find structural variants using the smoove workflow</description>
     <macros>
         <import>macro_lumpy_smoove.xml</import>
@@ -14,17 +14,22 @@
     @set_fasta_index@
     ln -s $normal_bam normal.bam &&
     ln -s $tumor_bam tumor.bam &&
-    
-    smoove call -x --name output
+    samtools index -@ \${GALAXY_SLOTS:-4} normal.bam &&
+    samtools index -@ \${GALAXY_SLOTS:-4} tumor.bam &&
+   
+    smoove call --name output
         #if $set_exclusion.choices=="yes":
             --exclude $bedmask
         #end if
-        --fasta reference.fa -p \${GALAXY_SLOTS:-4} normal.bam tumor.bam &&
-    gunzip output-smoove.vcf.gz
-    #if $prpos=="no":
-    && sed -i -E 's/;PRPOS=.+\tGT/\tGT/g' output-smoove.vcf
-    #end if
-    
+            --fasta reference.fa
+            --processes \${GALAXY_SLOTS:-4}
+            --genotype
+       #if $prpos=="no":
+            --removepr
+       #end if
+           normal.bam tumor.bam &&
+    ls -latr &&
+    gunzip output-smoove.genotyped.vcf.gz
 
     ]]></command>
     <inputs>
@@ -49,52 +54,51 @@
    </inputs>
 
     <outputs>
-        <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.vcf" />
+        <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.genotyped.vcf" />
     </outputs>
 
     <tests>
         <test>
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="chrI-ce11.fa"/>
-            <param name="normal_bam" value="celegans_1.bam"/>
-            <param name="tumor_bam" value="celegans_2.bam"/>
+            <param name="normal_bam" value="celegans_RG_1.bam"/>
+            <param name="tumor_bam" value="celegans_RG_2.bam"/>
             <param name="choices" value="yes"/>
             <param name="bedmask" value="exclude.bed"/>
             <param name="prpos" value="no"/>
-            <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="4"/>
+            <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="6"/>
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="chrI-ce11.fa"/>
-            <param name="normal_bam" value="celegans_1.bam"/>
-            <param name="tumor_bam" value="celegans_2.bam"/>
+            <param name="normal_bam" value="celegans_RG_1.bam"/>
+            <param name="tumor_bam" value="celegans_RG_2.bam"/>
             <param name="choices" value="no"/>
             <param name="prpos" value="no"/>
-            <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="4"/>
+            <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="6"/>
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="chrI-ce11.fa"/>
-            <param name="normal_bam" value="celegans_2.bam"/>
-            <param name="tumor_bam" value="celegans_1.bam"/>
+            <param name="normal_bam" value="celegans_RG_2.bam"/>
+            <param name="tumor_bam" value="celegans_RG_1.bam"/>
             <param name="choices" value="no"/>
             <param name="prpos" value="no"/>
-            <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="4"/>
+            <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="6"/>
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="chrI-ce11.fa"/>
-            <param name="normal_bam" value="celegans_1.bam"/>
-            <param name="tumor_bam" value="celegans_2.bam"/>
+            <param name="normal_bam" value="celegans_RG_1.bam"/>
+            <param name="tumor_bam" value="celegans_RG_2.bam"/>
             <param name="choices" value="no"/>
             <param name="prpos" value="yes"/>
-            <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="4"/>
+            <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="6"/>
         </test>
 
     </tests>
 
     <help>
-
 **smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves
 specificity by removing many spurious alignment signals that are indicative of low-level
 noise and often contribute to spurious calls.
@@ -105,17 +109,21 @@
 Currently, this Galaxy tool only wraps smoove for 2 samples (bam normal and tumor inputs),
 which translates in the command line::
 
-    <![CDATA[smoove call -x --name my-cohort --exclude $bed --fasta $fasta -p $threads /path/to/*.bam]]>
+    <![CDATA[smoove call --name my-cohort --exclude $bed --fasta $fasta -p $threads --genotype [--removepr] /path/to/*.bam]]>
 
-Note that the --genotype option which allows to stream smoove to svtyper is not implemented
-due to an error returned by svtyper in the smoove conda environment
 
 the --exclude $bed is highly recommended as it can be used to ignore reads that overlap
 problematic regions.
 
-A good set of regions for GRCh37 is https://github.com/hall-lab/speedseq/blob/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed
+A good set of regions for GRCh37 can be found here_
+
+.. _here: https://github.com/hall-lab/speedseq/blob/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed
+
 
-And for hg38 https://github.com/hall-lab/speedseq/blob/master/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed
+And a good set for GRCh38 can be found there_
+
+.. _there: https://github.com/hall-lab/speedseq/blob/master/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed
+
 
 smoove will::
 
@@ -130,20 +138,22 @@
     size as required by lumpy.
     
     4. stream output of lumpy directly into multiple svtyper processes for parallel-by-region
-    genotyping while lumpy is still running. This option in not currently implemented in Galaxy
+    genotyping while lumpy is still running.
     
-    5. sort, compress, and index final VCF.
+    5. sort, compress, and index final VCF (but this galaxy wrapper is uncompression the gzip_vcf output)
 
 **Input(s)**
 
-
-*BAM files*: One Bam for normal sample and one Bam for tumor sample.
-Only BAM alignments produced by BWA-mem have been tested with this tool
-
-*A bed file* describing the regions to exclude from the analysis
+* BAM files: One Bam for normal sample and one Bam for tumor sample. Only BAM alignments produced by BWA-mem have been tested with this tool
+    
+    .. class:: warningmark
+    
+    It is mandatory for proper run of svtyper that **BAM files contain read group information**,
+    ie the @RG tag is present and filled in each BAM
 
 
-*Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84)
+* A bed file describing the regions to exclude from the analysis
+* Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84)
 
 .. _repository: https://github.com/brentp/smoove
 
Binary file test-data/celegans_1.bam has changed
Binary file test-data/celegans_2.bam has changed
Binary file test-data/celegans_RG_1.bam has changed
Binary file test-data/celegans_RG_2.bam has changed
--- a/test-data/result-1.vcf	Wed Aug 26 05:48:01 2020 -0400
+++ b/test-data/result-1.vcf	Wed Aug 26 12:24:07 2020 -0400
@@ -1,10 +1,7 @@
 ##fileformat=VCFv4.2
-##contig=<ID=chrI,length=15072434>
-##smoove_version=0.2.5
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20200826
 ##reference=reference.fa
-##smoove_count_stats=tumor:2531,2421,134,276
-##smoove_count_stats=normal:2869,2691,194,304
-##source=LUMPY
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
@@ -22,8 +19,6 @@
 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
-##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
-##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
 ##ALT=<ID=DEL,Description="Deletion">
 ##ALT=<ID=DUP,Description="Duplication">
 ##ALT=<ID=INV,Description="Inversion">
@@ -35,5 +30,30 @@
 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal	tumor
-chrI	10416569	1	N	<DUP>	.	.	SVTYPE=DUP;STRANDS=-+:4;SVLEN=981;END=10417550;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;IMPRECISE;SU=4;PE=4;SR=0	GT:SU:PE:SR	./.:4:4:0	./.:0:0:0
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
+##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
+##contig=<ID=chrI,length=15072434>
+##smoove_version=0.2.5
+##smoove_count_stats=celegans-2:2531,2421,134,276
+##smoove_count_stats=celegans-1:2869,2691,194,304
+##source=LUMPY
+##bcftools_annotateVersion=1.10.2+htslib-1.10.2
+##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Aug 26 16:53:42 2020
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##bcftools_viewVersion=1.10.2+htslib-1.10.2
+##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Aug 26 16:53:42 2020
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	celegans-1	celegans-2
+chrI	10416569	1	N	<DUP>	170.7	.	SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=4;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69	1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43
--- a/test-data/result-2.vcf	Wed Aug 26 05:48:01 2020 -0400
+++ b/test-data/result-2.vcf	Wed Aug 26 12:24:07 2020 -0400
@@ -1,10 +1,7 @@
 ##fileformat=VCFv4.2
-##contig=<ID=chrI,length=15072434>
-##smoove_version=0.2.5
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20200826
 ##reference=reference.fa
-##smoove_count_stats=tumor:2531,2421,156,296
-##smoove_count_stats=normal:2869,2691,202,330
-##source=LUMPY
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
@@ -22,8 +19,6 @@
 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
-##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
-##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
 ##ALT=<ID=DEL,Description="Deletion">
 ##ALT=<ID=DUP,Description="Duplication">
 ##ALT=<ID=INV,Description="Inversion">
@@ -35,5 +30,30 @@
 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal	tumor
-chrI	10416569	1	N	<DUP>	.	.	SVTYPE=DUP;STRANDS=-+:4;SVLEN=981;END=10417550;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;IMPRECISE;SU=4;PE=4;SR=0	GT:SU:PE:SR	./.:4:4:0	./.:0:0:0
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
+##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
+##contig=<ID=chrI,length=15072434>
+##smoove_version=0.2.5
+##smoove_count_stats=celegans-2:2531,2421,156,296
+##smoove_count_stats=celegans-1:2869,2691,202,330
+##source=LUMPY
+##bcftools_annotateVersion=1.10.2+htslib-1.10.2
+##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Aug 26 16:54:42 2020
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##bcftools_viewVersion=1.10.2+htslib-1.10.2
+##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Aug 26 16:54:42 2020
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	celegans-1	celegans-2
+chrI	10416569	1	N	<DUP>	170.7	.	SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=4;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69	1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43
--- a/test-data/result-3.vcf	Wed Aug 26 05:48:01 2020 -0400
+++ b/test-data/result-3.vcf	Wed Aug 26 12:24:07 2020 -0400
@@ -1,10 +1,7 @@
 ##fileformat=VCFv4.2
-##contig=<ID=chrI,length=15072434>
-##smoove_version=0.2.5
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20200826
 ##reference=reference.fa
-##smoove_count_stats=tumor:2869,2691,202,330
-##smoove_count_stats=normal:2531,2421,156,296
-##source=LUMPY
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
@@ -22,8 +19,6 @@
 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
-##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
-##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
 ##ALT=<ID=DEL,Description="Deletion">
 ##ALT=<ID=DUP,Description="Duplication">
 ##ALT=<ID=INV,Description="Inversion">
@@ -35,5 +30,30 @@
 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal	tumor
-chrI	10416569	1	N	<DUP>	.	.	SVTYPE=DUP;STRANDS=-+:4;SVLEN=981;END=10417550;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;IMPRECISE;SU=4;PE=4;SR=0	GT:SU:PE:SR	./.:0:0:0	./.:4:4:0
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
+##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
+##contig=<ID=chrI,length=15072434>
+##smoove_version=0.2.5
+##smoove_count_stats=celegans-2:2531,2421,156,296
+##smoove_count_stats=celegans-1:2869,2691,202,330
+##source=LUMPY
+##bcftools_annotateVersion=1.10.2+htslib-1.10.2
+##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Aug 26 16:55:52 2020
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##bcftools_viewVersion=1.10.2+htslib-1.10.2
+##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Aug 26 16:55:52 2020
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	celegans-2	celegans-1
+chrI	10416569	1	N	<DUP>	170.7	.	SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=4;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43	1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69
--- a/test-data/result-4.vcf	Wed Aug 26 05:48:01 2020 -0400
+++ b/test-data/result-4.vcf	Wed Aug 26 12:24:07 2020 -0400
@@ -1,10 +1,7 @@
 ##fileformat=VCFv4.2
-##contig=<ID=chrI,length=15072434>
-##smoove_version=0.2.5
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20200826
 ##reference=reference.fa
-##smoove_count_stats=normal:2869,2691,202,330
-##smoove_count_stats=tumor:2531,2421,156,296
-##source=LUMPY
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
@@ -35,5 +32,28 @@
 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal	tumor
-chrI	10416569	1	N	<DUP>	.	.	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+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
+##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
+##contig=<ID=chrI,length=15072434>
+##smoove_version=0.2.5
+##smoove_count_stats=celegans-1:2869,2691,202,330
+##smoove_count_stats=celegans-2:2531,2421,156,296
+##source=LUMPY
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##bcftools_viewVersion=1.10.2+htslib-1.10.2
+##bcftools_viewCommand=view -O z -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Aug 26 16:57:03 2020
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	celegans-1	celegans-2
+chrI	10416569	1	N	<DUP>	170.7	.	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