Analyses of Indels

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.

Dataset	Freebayes	Haplotyecaller	PINDEL	Platypus	RTG	Samtools	SGA
Biallelic
Left trim	27069	1	0	0	0	0	15047
Left aligned	3	1	1	0	12262	2	1892
Multi-allelic
Left trim	40782	0	0	0	374
Left aligned	1892	0	0	0	1329	1	0
Right trimmed	0	0	0	25393	0	11	0
Duplicate variants	0	1	155	3143	286	8	7541

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