Multiinfo

tests/test_data/float_info.tsv

@@ -0,0 +1,2 @@
+chrom	pos	freq
+22	18644673	0.042

tests/test_data/info.tsv

@@ -1,2 +1,3 @@
+chrom	pos	value
 10	100	0
 22	18644673	2

tests/test_data/info2.tsv

@@ -1 +1,2 @@
+chrom	pos	value
 chr1	168192360	0

tests/test_data/info2_cleared.vcf

@@ -0,0 +1,83 @@
+##fileformat=VCFv4.0
+##source=VarscanSomatic
+##reference=ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests/GRCh37-lite.fa.gz
+##phasing=none
+##center=genome.wustl.edu
+##FILTER=<ID=PASS,Description="Passed all filters">
+##FILTER=<ID=VarscanHighConfidenceIndel,Description="Filter description">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality for reads supporting alleles">
+##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
+##FORMAT=<ID=GQ,Number=.,Type=Integer,Description="Conditional Phred-scaled genotype quality">
+##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel with respect to the genome's ancestor">
+##FORMAT=<ID=FA,Number=1,Type=Float,Description="Fraction of reads supporting ALT">
+##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample genotype filter">
+##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
+##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
+##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
+##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
+##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic score between 0 and 255">
+##source=Strelka
+##FORMAT=<ID=FDP,Number=1,Type=Integer,Description="Number of basecalls filtered from original read depth for tier1">
+##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Number of reads with deletions spanning this site at tier1">
+##FORMAT=<ID=SUBDP,Number=1,Type=Integer,Description="Number of reads below tier1 mapping quality threshold aligned across this site">
+##FORMAT=<ID=AU,Number=2,Type=Integer,Description="Number of 'A' alleles used in tiers 1,2">
+##FORMAT=<ID=CU,Number=2,Type=Integer,Description="Number of 'C' alleles used in tiers 1,2">
+##FORMAT=<ID=GU,Number=2,Type=Integer,Description="Number of 'G' alleles used in tiers 1,2">
+##FORMAT=<ID=TU,Number=2,Type=Integer,Description="Number of 'T' alleles used in tiers 1,2">
+##FORMAT=<ID=DP2,Number=1,Type=Integer,Description="Read depth for tier2">
+##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2">
+##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2">
+##FORMAT=<ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2">
+##FORMAT=<ID=DP50,Number=1,Type=Float,Description="Average tier1 read depth within 50 bases">
+##FORMAT=<ID=FDP50,Number=1,Type=Float,Description="Average tier1 number of basecalls filtered from original read depth within 50 bases">
+##FORMAT=<ID=SUBDP50,Number=1,Type=Float,Description="Average number of reads below tier1 mapping quality threshold aligned across sites within 50 bases">
+##INFO=<ID=QSI,Number=1,Type=Integer,Description="Quality score for any somatic variant, ie. for the ALT haplotype to be present at a significantly different frequency in the tumor and normal">
+##INFO=<ID=TQSI,Number=1,Type=Integer,Description="Data tier used to compute QSI">
+##INFO=<ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}.">
+##INFO=<ID=QSI_NT,Number=1,Type=Integer,Description="Quality score reflecting the joint probability of a somatic variant and NT">
+##INFO=<ID=TQSI_NT,Number=1,Type=Integer,Description="Data tier used to compute QSI_NT">
+##INFO=<ID=SGT,Number=1,Type=String,Description="Most likely somatic genotype excluding normal noise states">
+##INFO=<ID=RU,Number=1,Type=String,Description="Smallest repeating sequence unit in inserted or deleted sequence">
+##INFO=<ID=RC,Number=1,Type=Integer,Description="Number of times RU repeats in the reference allele">
+##INFO=<ID=IC,Number=1,Type=Integer,Description="Number of times RU repeats in the indel allele">
+##INFO=<ID=IHP,Number=1,Type=Integer,Description="Largest reference interupted homopolymer length intersecting with the indel">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=OVERLAP,Number=0,Type=Flag,Description="Somatic indel possibly overlaps a second indel.">
+##FILTER=<ID=DP,Description="Greater than 3.0x chromosomal mean depth in Normal sample">
+##FILTER=<ID=Repeat,Description="Sequence repeat of more than 8x in the reference sequence">
+##FILTER=<ID=iHpol,Description="Indel overlaps an interupted homopolymer longer than 14x in the reference sequence">
+##FILTER=<ID=BCNoise,Description="Average fraction of filtered basecalls within 50 bases of the indel exceeds 0.3">
+##FILTER=<ID=QSI_ref,Description="Normal sample is not homozygous ref or sindel Q-score < 30, ie calls with NT!=ref or QSI_NT < 30">
+##source=Pindel
+##FILTER=<ID=PindelSomaticCalls,Description="Filter description">
+##FILTER=<ID=PindelVafFilter,Description="Filter description">
+##FILTER=<ID=PindelReadSupport,Description="Filter description">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
+##source=GatkSomaticIndel
+##fileDate=20160321
+##INFO=<ID=QSS,Number=1,Type=Integer,Description="Quality score for any somatic snv, ie. for the ALT allele to be present at a significantly different frequency in the tumor and normal">
+##INFO=<ID=TQSS,Number=1,Type=Integer,Description="Data tier used to compute QSS">
+##INFO=<ID=QSS_NT,Number=1,Type=Integer,Description="Quality score reflecting the joint probability of a somatic variant and NT">
+##INFO=<ID=TQSS_NT,Number=1,Type=Integer,Description="Data tier used to compute QSS_NT">
+##FILTER=<ID=VarFilterSnv,Description="Filter description">
+##FILTER=<ID=FalsePositiveVcf,Description="Filter description">
+##FILTER=<ID=FalsePositive,Description="Filter description">
+##FILTER=<ID=SomaticScoreMappingQuality,Description="Filter description">
+##FILTER=<ID=IntersectionFailure,Description="Variant callers do not agree on this position">
+##FILTER=<ID=SpanDel,Description="Fraction of reads crossing site with spanning deletions in either sample exceeeds 0.75">
+##FILTER=<ID=QSS_ref,Description="Normal sample is not homozygous ref or ssnv Q-score < 15, ie calls with NT!=ref or QSS_NT < 15">
+##FORMAT=<ID=TLOD,Number=.,Type=Float,Description="Log of (likelihood tumor event is real / likelihood event is sequencing error)">
+##FILTER=<ID=REJECT,Description="Rejected as a confident somatic mutation by MuTect">
+##FILTER=<ID=VarscanHighConfidence,Description="Filter description">
+##FILTER=<ID=PASS,Description="Passed all filters">
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Mapping quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
+chr1	168192360	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609

tests/test_data/info2_input.vcf

@@ -80,4 +80,4 @@
 ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Number of MAPQ == 0 reads covering this record">
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-chr1	168192360	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
+chr1	168192360	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC;MQ0=5	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609

tests/test_data/info2_output.vcf

@@ -77,7 +77,7 @@
 ##FILTER=<ID=REJECT,Description="Rejected as a confident somatic mutation by MuTect">
 ##FILTER=<ID=VarscanHighConfidence,Description="Filter description">
 ##FILTER=<ID=PASS,Description="Passed all filters">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Number of MAPQ == 0 reads covering this record">
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Mapping quality">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
 chr1	168192360	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC;MQ0=0	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609

tests/test_data/info3.tsv

@@ -1 +1,2 @@
+chrom	pos	value
 22	18644673	asdffdsa

tests/test_data/info_overwrite.vcf

@@ -77,6 +77,6 @@
 ##FILTER=<ID=REJECT,Description="Rejected as a confident somatic mutation by MuTect">
 ##FILTER=<ID=VarscanHighConfidence,Description="Filter description">
 ##FILTER=<ID=PASS,Description="Passed all filters">
-##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
+##INFO=<ID=CSQ,Number=1,Type=String,Description="CSQ annotation">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
 22	18644673	.	C	T	.	.	CSQ=2	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609