09 Outputs

Output .vcf Files

summary.vcf

Output summary VCF containing detailed information regarding each query and truth input variant. Please note that homozygous variants are split into two heterozygous variants prior to vcfdist evaluation.

FORMAT Tag	Name	Type	Description
GT	GenoType	string	Genotype of the current variant.
BD	Benchmarking Decision	categorical	Benchmarking decision classification of the current variant (TP/FP/FN).
BC	Benchmarking Credit	float	Benchmarking credit allocated to the current variant in the range [0.0, 1.0].
RD	Reference edit Distance	integer	Edit distance between the reference and truth sequences for this sync group.
QD	Query edit Distance	integer	Edit distance between the query and truth sequences for this sync group.
BK	Benchmarking Kategory	categorical	GA4GH category is assigned to 'gm' if credit == 1 (genotype match), 'lm' if credit > 0 (local match), or else '.' (no match).
QQ	Quality	integer	Variant PHRED-scaled quality score.
SC	SuperCluster	integer	0-based index of supercluster in which this variant occurs, on this contig.
SG	Sync Group	integer	0-based index of the current variant's sync group in this supercluster on this haplotype. Variants in the same sync group are considered complex, evaluated together, and assigned a single credit value.
PS	Phase Set	integer	Phase set identifier for the current variant.
PB	Phase Block	integer	0-based index of current phase block in this contig.
BS	Block State	integer	Phasing state of the current phase block, which determines the truth-to-query haplotype mappings: 0 = T1Q1:T2Q2, 1 = T1Q2:T2Q1.
FE	Flip Error	integer	Whether the current supercluster's phasing is flipped (1) or not (0).

For full false positive (FP) variants where credit is 0.0, RD and QD are missing (.) because the query variant is never aligned and there is no corresponding truth variant.

orig-query.vcf, orig-truth.vcf

Original query and truth VCFs, as parsed by vcfdist.

query.vcf, truth.vcf

Output query and truth VCFs, (optionally standardized by vcfdist using --realign).

Output .tsv Files

.tsv, or tab-separated value files, are a simple text-based format used to store vcfdist's output.

Variants

query.tsv, truth.tsv

Reports detailed information regarding each variant.

Column	Type	Description
CONTIG	string	Name of the contig on which this variant is located.
POS	integer	0-based index of genomic position where this variant occurs on this contig. Insertions occur before this base.
HAP	integer	Variant occurs on this haplotype (0 or 1 if diploid).
REF	string	Reference allele of this variant.
ALT	string	Alternate allele of this variant.
QUAL	float	Quality score of this variant.
TYPE	categorical	Type of variant (REF/SNP/INS/DEL/CPX).
ERR_TYPE	categorical	Classification error type (TP/FP/FN).
CREDIT	float	Fraction of partial credit (in terms of correctness) that this variant received. --credit-threshold determines whether it is a true or false positive.
CLUSTER	integer	0-based index of the cluster on the current haplotype of this contig containing this variant.
SUPERCLUSTER	integer	0-based index of the supercluster on this contig containing this variant.
SYNC_GROUP	integer	0-based index of credit grouping for variants on this haplotype and within this supercluster.
REF_DIST	integer	Edit distance between the reference and truth sequences for the current sync group.
QUERY_DIST	integer	Edit distance between the query and truth sequences for the current sync group.
LOCATION	categorical	Location of variant relative to BED regions (INSIDE/OUTSIDE/BORDER/OFF_CTG)

For full false positive (FP) variants where credit is 0.0, REF_DIST and QUERY_DIST set to 0 because the query variant is never aligned and there is no corresponding truth variant.

Clusters

superclusters.tsv

Reports the size, location, and composition of each supercluster.

Column	Type	Description
CONTIG	string	Name of the contig on which this supercluster is located.
SUPERCLUSTER	integer	0-based index of supercluster on this contig.
START	integer	0-based leftmost genomic position of this supercluster on this contig, inclusive.
STOP	integer	0-based rightmost genomic position of this supercluster on this contig, exclusive
SIZE	integer	Size of this supercluster, STOP-START.
QUERY1_VARS	integer	Number of variants from query haplotype 0 within this supercluster.
QUERY2_VARS	integer	Number of variants from query haplotype 1 within this supercluster.
TRUTH1_VARS	integer	Number of variants from truth haplotype 0 within this supercluster.
TRUTH2_VARS	integer	Number of variants from truth haplotype 1 within this supercluster.
ORIG_ED	integer	The minimum edit distance of this supercluster, assuming the original reported phasing is correct.
SWAP_ED	integer	The minimum edit distance of this supercluster, assuming the phasing of all variants is flipped.
PHASE_STATE	integer	Current phase block phasing state at this supercluster (0 = T1Q1:T2Q2, 1 = T1Q2: T2Q1).
SC_PHASE	categorical	Phase state of this supercluster, based on minimum edit distances.
PHASE_SET	integer	Phase set of this supercluster (PS tag input, genomic position of leftmost variant in phase set).
PHASE_BLOCK	integer	0-based index of phase block within this contig.
FLIP_ERROR	integer	Whether this supercluster is considered a flip error (1) or not (0).

Precision and Recall

precision-recall-summary.tsv

High-level precision/recall overview of SNP/INDEL/SV performance. For each category, there is one line for performance at the chosen minimum quality score, and one line for the quality score threshold that results in the best performance.

Column	Type	Description
VAR_TYPE	categorical	Variant type category. SNP for substitutions, INDEL for variants smaller than --sv-threshold, and SV for larger variants.
MIN_QUAL	integer	Variants above this minimum quality score are used to calculate the performance metrics on this line.
TRUTH_TP	integer	Total measured true positive truth variants in this variant category.
QUERY_TP	integer	Total measured true positive query variants in this variant category.
TRUTH_FN	integer	Total measured false negative truth variants in this variant category.
QUERY_FP	integer	Total measured false positive query variants in this variant category.
PREC	float	Measured variant calling precision in the range [0.0, 1.0]: QUERY_TP / (QUERY_FP + QUERY_TP).
RECALL	float	Measured variant calling recall in the range [0.0, 1.0]: TRUTH_TP / (TRUTH_TP + TRUTH_FN).
F1_SCORE	float	Measured variant calling F1 score in the range [0.0, 1.0]: (2PRECRECALL) / (PREC + RECALL).
F1_QSCORE	float	PHRED-scaled measure of F1 score: -10*log10(1-F1_SCORE).

precision-recall.tsv

For each category (SNP/INDEL/SV), there is one line reporting the precison/recall performance at each possible quality score.

Column	Type	Description
VAR_TYPE	categorical	Variant type category. SNP for substitutions, INDEL for variants smaller than --sv-threshold, and SV for larger variants.
MIN_QUAL	integer	Variants above this minimum quality score are used to calculate the performance metrics on this line.
PREC	float	Measured variant calling precision in the range [0.0, 1.0]: QUERY_TP / (QUERY_FP + QUERY_TP).
RECALL	float	Measured variant calling recall in the range [0.0, 1.0]: TRUTH_TP / (TRUTH_TP + TRUTH_FN).
F1_SCORE	float	Measured variant calling F1 score in the range [0.0, 1.0]: (2PRECRECALL) / (PREC + RECALL).
F1_QSCORE	float	PHRED-scaled measure of F1 score: -10*log10(1-F1_SCORE).
TRUTH_TOTAL	integer	Total truth variants in this variant category.
TRUTH_TP	integer	Total measured true positive truth variants in this variant category.
TRUTH_FN	integer	Total measured false negative truth variants in this variant category.
QUERY_TOTAL	integer	Total query variants in this variant category.
QUERY_TP	integer	Total measured true positive query variants in this variant category.
QUERY_FP	integer	Total measured false positive query variants in this variant category.

Phasing Analysis

phase-blocks.tsv

Reports the size, location, and composition of each phase block.

Column	Type	Description
CONTIG	string	Name of the contig which contains the current phase block.
PHASE_BLOCK	integer	0-based index of this phase block within the contig.
START	integer	0-based index of the leftmost genomic position within current phase block, inclusive.
STOP	integer	0-based index of the rightmost genomic position within current phase block, exclusive.
SIZE	integer	Size of the current phase block.
SUPERCLUSTERS	integer	Total superclusters comprising this phase block.
FLIP_ERRORS	integer	Total flip errors that occur within this phase block.
SWITCH_ERRORS	integer	Total switch errors that occur within this phase block.

phasing-summary.tsv

High-level summary of phasing performance.

Column	Type	Description
PHASE_BLOCKS	integer	Total phase blocks, across all evaluated contigs.
SWITCH_ERRORS	integer	Total switch errors, across all evaluated contigs.
FLIP_ERRORS	integer	Total flip errors, across all evaluated contigs.
NG_50	integer	NG50 (break regions on new phase block), across all evaluated contigs.
SWITCH_NGC50	integer	Switch NGC50 (break regions on new phase block or switch error), across all evaluated contigs.
SWITCHFLIP_NGC50	integer	Switchflip NGC50 (break regions on new phase block, switch error, or flip error), across all evaluated contigs.

switchflips.tsv

Detailed breakdown of all switch and flip errors.

Column	Type	Description
CONTIG	string	Contig on which phasing error occurred.
START	integer	0-based index of leftmost genomic position where phasing error could have occurred.
STOP	integer	0-based index of rightmost genomic position where phasing error could have occurred.
SWITCH_TYPE	categorical	Type of phasing error.
SUPERCLUSTER	integer	0-based index of supercluster on this contig where the phasing error occurred.
PHASE_BLOCK	integer	0-based index of phase block on this contig which the phasing error occurred within.

Alignment Distance

distance-summary.tsv

High-level alignment distance overview of SNP/INDEL performance. For each category (SNP/INDEL/ALL), there is one line for performance at the minimum, best, and maximum quality score threshold.

Column	Type	Description
VAR_TYPE	categorical	Variant category considered on this line (ALL/SNP/INS/DEL/INDEL).
MIN_QUAL	integer	Minimum variant quality considered.
EDIT_DISTANCE	integer	Total edit distance from truth sequence after query variants above MIN_QUAL are applied.
DISTINCT_EDITS	integer	Total number of edits from truth sequence after query variants above MIN_QUAL are applied.
ED_QSCORE	float	PHRED-scaled measure of query sequence quality in terms of edit distance: -10*log10(EDIT_DISTANCE / ORIG_EDIT_DISTANCE), where ORIG_EDIT_DISTANCE is the query edit distance from the truth sequence when no query variants are applied.
DE_QSCORE	float	PHRED-scaled measure of query sequence quality in terms of distinct edits: -10*log10(DISTINCT_EDITS / TRUTH_TOTAL), where TRUTH_TOTAL is total number of truth variants.
ALN_QSCORE	float	PHRED-scaled measure of query sequence quality in terms of alignment score: -10*log10(ALN_SCORE / ORIG_ALN_SCORE), where ORIG_ALN_SCORE is the query alignment score (to the truth sequence) when no query variants are applied.

distance.tsv

There is one line reporting the alignment distance performance at each possible quality score.

Column	Type	Description
MIN_QUAL	integer	Minimum variant quality considered.
SUB_DE	integer	Total number of substitution edits during alignment.
INS_DE	integer	Total number of insertion edits during alignment.
DEL_DE	integer	Total number of deletion edits during alignment.
SUB_ED	integer	Total number of bases substituted during alignment.
INS_ED	integer	Total number of bases inserted during alignment.
DEL_ED	integer	Total number of bases deleted during alignment.
DISTINCT_EDITS	integer	Total number of edits from truth sequence after query variants above MIN_QUAL are applied.
EDIT_DIST	integer	Total edit distance from truth sequence after query variants above MIN_QUAL are applied.
ALN_SCORE	integer	Smith-Waterman alignment score of query sequence to truth sequence, after applying query variants above MIN_QUAL.
ALN_QSCORE	float	PHRED-scaled measure of query sequence quality in terms of alignment score: -10*log10(ALN_SCORE / ORIG_ALN_SCORE), where ORIG_ALN_SCORE is the query alignment score (to the truth sequence) when no query variants are applied.

edits.tsv

This file reports for each edit (where called query sequence differs from truth sequence) the contig, pos, hap, len, supercluster, and the quality range for which these edits occur.

Column	Type	Description
CONTIG	string	Name of the contig on which this edit occurs.
START	integer	0-based genomic position on this contig where this edit is located.
HAP	integer	Haplotype on which this edit occurs.
TYPE	categorical	Edit category type (SNP/INS/DEL).
SIZE	integer	Size of the edit, in terms of reference or query bases affected.
SUPERCLUSTER	integer	0-based index of the supercluster containing the edit, on this contig.
MIN_QUAL	integer	The edit is present at and above this quality score.
MAX_QUAL	integer	The edit is present below this quality score.

Output .txt Files

parameters.txt

This file stores all internal and command-line parameters used by vcfdist (for reproducibility and debugging purposes). Each line stores a single parameter in the format parameter = value.