WISARD[wɪzərd]
Workbench for Integrated Superfast Association study with Related Data
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Mendelian error

Mendelian error can be evaluated for family-based samples and WISARD provides a simple function to calculate Mendelian error rates by using --mendel option.

Investigate dataset-level Mendelian error rate C:\Users\WISARD> wisard --bed test_miss0.bed --mendel --out result_mendel

Running WISARD with --mendel option produces three output files: [prefix].family.res, [prefix].sample.res and [prefix].variant.res.

Output files [top]

Columns in each output file have a different meaning as follows:

  • [prefix].mendel.family.res
mendel.family.res is... A result of analysis of family-wise Mendelian transmission error (TSV)
Column Format Modifier Description
FID string NONE Family ID of Mendelian error investigated
ERROR integer NONE Number of alleles have Mendelian error for the family
AVAIL integer NONE Number of called alleles for the family
PROP real NONE Mendelian error rate for the family
  • [prefix].mendel.sample.res
mendel.sample.res is... A result of analysis of sample-wise Mendelian transmission error (TSV)
Column Format Modifier Description
FID string NONE Family ID of the sample of Mendelian error investigated
IID string NONE Individual ID of Mendelian error investigated
ERROR integer NONE Number of alleles have Mendelian error for the sample
AVAIL integer NONE Number of called alleles for the sample
PROP real NONE Mendelian error rate for the sample
  • [prefix].mendel.variant.res
mendel.variant.res is... A result of analysis of variant-wise Mendelian transmission error (TSV)
Column Format Modifier Description
CHR real NONE Mendelian error rate for the sample
VARIANT real NONE Mendelian error rate for the sample
POS real NONE Mendelian error rate for the sample
ALT real NONE Mendelian error rate for the sample
ANNOT real NONE Mendelian error rate for the sample
ERROR integer NONE Number of alleles have Mendelian error for the variant
AVAIL integer NONE Number of called alleles for the variant
PROP real NONE Mendelian error rate for the variant

Filtering individuals/variants with Mendelian error rate [top]

It filters sample(s) samples or families by the portion of genotypes having Mendelian transmission error.

NOTE!
The parameter of this option supports range type parameter
Exclude families with Mendelian error rate>=50% C:\Users\WISARD> wisard --filmendelfam ">=0.5" --ped test_miss0.ped
Include families with 10% C:\Users\WISARD> wisard --incmendelfam "(0.1,0.25]" --ped test_miss0.ped
Exclude samples with Mendelian error rate>20% C:\Users\WISARD> wisard --filmendelsamp ">0.2" --ped test_miss0.ped
Include samples with Mendelian error rate C:\Users\WISARD> wisard --incmendelsamp "<0.1" --ped test_miss0.ped
NOTE!
The parameter of this option supports range type parameter
Exclude variants with Mendelian error rate C:\Users\WISARD> wisard --filmendelvar "[0,0.1)" --ped test_miss0.ped
Include variants with Mendelian error rate C:\Users\WISARD> wisard --incmendelvar "<=0.01" --ped test_miss0.ped


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Last modified : 2017-08-29 13:03:01