diff test-data/result-1.vcf @ 3:65b400409455 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"

--- 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