Family Analysis

FATHER MOTHER INHERITANCE
SELECT VARIANTS FROM EXCLUDE VARIANTS FROM
INDIVIDUALS:

SNP LIST:
GROUPS:

SAVED GENE LIST:

GENE LIST:
Exclude individuals:

EXCLUDE SNP LIST:
EXCLUDE GROUPS:

EXCLUDE SAVED GENE LIST:

EXCLUDE GENE LIST:
MUTATION TYPE:
CHR:

POS:
VARIANT EFFECT FUNCTIONAL CLASS IMPACT
DBSNP BUILD:


EXCLUDE VARIANTS AT VARISNP
READ DEPTH:

QUAL:
VARIANTS PER GENE:
SHOW ONLY VARIANTS PRESENT IN COMMON GENES BETWEEN ALL THE INDIVIDUALS SELECTED
SHOW ONLY VARIANTS AT EXACTLY SAME POSITION BETWEEN ALL THE INDIVIDUALS SELECTED
EXCLUDE ALL VARIANTS PRESENT IN LATEST DBSNP BUILD
SHOW ONLY VARIANTS PRESENT AT HGMD

FREQUENCIES

1000 GENOMES FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN 1000GENOMES
DBSNP FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN DBSNP
ESP6500 FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN EXOME SEQUENCING PROJECT

SCORES

SIFT SCORE

EXCLUDE VARIANTS WITHOUT SIFT SCORE
POLYPHEN2 SCORE

EXCLUDE VARIANTS WITHOUT POLYPHEN SCORE
CADD

EXCLUDE VARIANTS WITHOUT CADD SCORE
MCAP

OMIM
CGD
CGD MANIFESTATION
HGMD
Name User Created on Options
לען shaytzur July 12, 2017, 9 a.m. EditDelete

Example of genotype information:

0/1:0.45:10,12:22:99:211,0,262

GT:AB:AD:DP:GQ:PL

GT: Genotype

Genotype, encoded as allele values separated by either of ”/” or “|”. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1, 1|0, or 1/2, etc. For haploid calls, e.g. on Y, male non-pseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, ”.” should be specified for each missing allele in the GT field (for example "./." for a diploid genotype and "." for haploid genotype). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes)

AB: Allele balance for each het genotype

The allele balance (fraction of ref bases over ref + alt bases) across all bialleleic het-called samples

AD: Allelic depths for the ref and alt alleles in the order listed

The depth of coverage of each VCF allele in this sample.

DP: Read Depth (only filtered reads used for calling) GQ: Genotype Quality

Conditional genotype quality, encoded as a phred quality -10log_10p(genotype call is wrong, conditioned on the site's being variant) (Float)

PL: Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification

The phred-scaled genotype likelihoods rounded to the closest integer (and otherwise defined precisely as the GL field) (Integers)

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Genes:

Genes at Omim

Genes at Clinical Genomics Database