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Variant-level Summary

Related options : --variantsummary, --indel, --monotone, --singleton, --doubleton, --popuniq, --famuniq

WISARD provides several helpful measures for variants in each chromosome. This section describes about

Variant summary
- Output file
Detecting monotone/singleton/doubleton
Detecting family-specific variants
Detecting population-specific variants

Variant summary [top]

WISARD can provide a summary for variants in each chromosome, and it is produced with --variantsummary option. If --indel option is added, the summary for each chromosome includes information about indel and substitution.

Running WISARD with --variantsummary option provides the following information for variants in each chromosome:

Minimum/maximum physical position of variants
Number of variants
Number of monotones/singletons/doubletons

Running WISARD with --variantsummary and --indel options provides the following information for variants in each chromosome:

Number of insertions
Length of shortest/longest insertion
Average length of insertions
Number of deletions
Length of shortest/longest deletion
Average length of deletions
Number of substitutions

Example: Generate variant summary for test_miss0.bed C:\Users\WISARD> wisard --bed test_miss0.bed --indel --variantsummary --out res_variant_summary

Output file

From this code, summary.variant.res is generated and the meaning of each column is

Column	Format	Modifier	Description
*summary.variant.res* is...			A chromosome-wise summary for the various information from variants (TSV)
CHR	1~22/X/Y/Mt/Un	NONE	Target chromosome
MINPOS	integer	NONE	Minimally observed physical position for current chromosome in the dataset
MAXPOS	integer	NONE	Maximally observed physical position for current chromosome in the dataset
NSNV	integer	NONE	Number of Single Nucleotide Variants in current chromosome
NMONO	integer	NONE	Number of monotone variants in current chromosome
NSINGLETON	integer	NONE	Number of singleton variants in current chromosome
NDOUBLETON	integer	NONE	Number of doubleton variants in current chromosome
NSUB	real	--indel	Number of substitutions in current chromosome
NINS	real	--indel	Number of insertions in current chromosome
MININS	real	--indel	A length of shortest insertion in current chromosome
MAXINS	real	--indel	A length of longest insertion in current chromosome
AVGINS	real	--indel	An average length of insertions in current chromosome
NDEL	real	--indel	Number of deletions in current chromosome
MINDEL	real	--indel	A length of shortest deletion in current chromosome
MAXDEL	real	--indel	A length of longest deletion in current chromosome
AVGDEL	real	--indel	An average length of deletions in current chromosome

Detecting monotone/singleton/doubleton [top]

WISARD provides options to find out monotone (Have no alternative allele), singleton(single alternative allele in the dataset) and doubleton(two alternative alleles in the dataset). Monotone is not informative for genetic association analysis. Central limit theorem is hardly met for singletone and doubleton, and single variant analysis with them has large false negative/positive finding. Therefore, it is better to remove monotone, singleton and doubleton from the analysis.

Find out monotone variants C:\Users\WISARD> wisard --bed test_miss0.bed --monotone --out res_monotone_variants

Find out singleton variants C:\Users\WISARD> wisard --bed test_miss0.bed --singleton --out res_singleton_variants

Find out doubleton variants C:\Users\WISARD> wisard --bed test_miss0.bed --doubleton --out res_doubleton_variants

Detecting family-specific variants [top]

Some variants are family-specific: i.e., minor alleles are observed only for individuals in a single family. Runnging WISARD with --famuniq option provides summary about the family-specific variants.

Find out family-specific variants C:\Users\WISARD> wisard --bed test_miss0.bed --famuniq --out res_famuniq_variants

Column	Format	Modifier	Description
*variant.famuniq.res* is...			A list of family-specific variants (TSV)
CHR	integer	--set	Number of variants in the group
VARIANT	integer	--set	Number of variants in the group
POS	integer	--set	Number of variants in the group
ALT	integer	--set	Number of variants in the group
ANNOT	integer	--set	Number of variants in the group
FID	string	NONE	Family ID having that variant
COUNT	string	NONE	Minor allele count for that varinat

Detecting population-specific variants [top]

Some variants are population-specific: i.e., minor alleles are observed only for individuals in a single population. Runnging WISARD with --popuniq option provides summary about the population-specific variants. Note that this option requires an assignment of population group for samples. To understand this, refer this section.

Find out population-specific variants C:\Users\WISARD> wisard --bed test_miss0.bed --sampvar test_miss0_phen.txt --popuniq region --out res_popuniq_variants

Column	Format	Modifier	Description
*variant.popuniq.res* is...			A list of population-specific variants (TSV)
CHR	string	NONE	Minor allele count for that varinat
VARIANT	string	NONE	Minor allele count for that varinat
POS	string	NONE	Minor allele count for that varinat
ALT	string	NONE	Minor allele count for that varinat
ANNOT	string	NONE	Minor allele count for that varinat
POP_ID	string	NONE	Population ID having that variant
COUNT	string	NONE	Minor allele count for that varinat

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Last modified : 2017-08-30 18:41:15