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=Motivation=
This wiki page will details the useful steps in analysing Indels. In particular it is to help the group in understanding the issues and perform the analyses quickly without reinventing the wheel.
=Tools=
You can download vt and have some working knowledge of PERL to do stuff that vt does not support.
=Coding regions=
The proportion of frameshift Indels amongst coding region indels is a potential indicator of quality.
=STR =
Annotation of STRs is really important. Show example of a deceptive single base pair variant
==Normalization==
Indel representation is not unique, you should normalize them and remove duplicates.
==Annotation of Indels==
==Examining Mendelian Errors==
==Useful to have call sets from several different callers==
==Concordance==
Can check concordance of genotypes between callers
==Overlapping percentages with known data sets==
With Mills
with dbSNP
with exome chips
with genotyping chips if available
==Useful stratifying features==
AF - rare versus common
Indel length - computed naively versus tract length
Allele frequency bins
Type of Indels - homopolymer types and STR types and isolated
Adjacent SNPs
Adjacent MNPs
Clumping variants
==Other useful evaluations==
genotype likelihood concordance
concordance stratified by indel length or tract length
mendelian concordance by tract length
This wiki page will details the useful steps in analysing Indels. In particular it is to help the group in understanding the issues and perform the analyses quickly without reinventing the wheel.
=Tools=
You can download vt and have some working knowledge of PERL to do stuff that vt does not support.
=Coding regions=
The proportion of frameshift Indels amongst coding region indels is a potential indicator of quality.
=STR =
Annotation of STRs is really important. Show example of a deceptive single base pair variant
==Normalization==
Indel representation is not unique, you should normalize them and remove duplicates.
==Annotation of Indels==
==Examining Mendelian Errors==
==Useful to have call sets from several different callers==
==Concordance==
Can check concordance of genotypes between callers
==Overlapping percentages with known data sets==
With Mills
with dbSNP
with exome chips
with genotyping chips if available
==Useful stratifying features==
AF - rare versus common
Indel length - computed naively versus tract length
Allele frequency bins
Type of Indels - homopolymer types and STR types and isolated
Adjacent SNPs
Adjacent MNPs
Clumping variants
==Other useful evaluations==
genotype likelihood concordance
concordance stratified by indel length or tract length
mendelian concordance by tract length
