SVProps Output Header Definitions?

[David McBay]

Hi, we're trying to understand the SVprops output but can't find the definitions anywhere. These are our best guesses, can somebody please correct us/fill in the gaps! 

chr chromosome

start start position

chr2 chromosome 2 (if applicable)

end end position

id unique SV id

size size of event in bp

vac variant allele count (reads)

vaf variant allele frequency

singleton N/A if event present in multiple samples or sample name if only present in one

missingrate ?

svtype type of SV (DEL, INS, INV, BND, DUP)

ct ?

precise 1 if event is included in split read?

ci ?

inslen insertion length?

homlen homology length?

ce ?

refgq reference genotype quality?

altgq alternative genotype quality?

gqsum ?

rdratio ?

medianrc ?

refratio ?

altratio ?

maxaltratio ?

PEsupport paired ends

SRsupport split reads

supportsum ?

Cheers, 
David

[Tobias Rausch]

Hi David,

The primary purpose of SV props is to create a feature matrix for machine learning approaches to filter germline SVs. For very large cohorts such as 1000 Genomes or some of the large clinical resequencing cohorts this is a viable alternative to delly's default germline SV filter if and only if a good training set is available.

Thus, svprops generates mostly some site statistics across all samples and we usually first recalibrate the GQs for such large cohorts using:

https://github.com/tobiasrausch/vcfaid

./src/gq -g 30 -v output.vcf.gz input.vcf.gz

... then the output additionally includes HWE, inbreeding coefficients and some other metrics.

I am still updating some of the output fields of svprops but here is a brief explanation:

vac variant allele count  (across all samples)

vaf variant allele frequency (across all samples)

singleton N/A if present in multiple samples or sample name if only present in one

missingrate how many samples have a missing genotype (useful after GQ calibration)

ct Delly's INFO:CT

precise 1 if INFO:PRECISE

ci Delly's INFO:CIPOS

inslen insertion length

homlen homology length

ce Delly's INFO:CE 

refgq median reference genotype quality for all SV non-carriers (GT==0/0)

altgq median alternative genotype quality for het. SV carriers

gqsum total GQ sum (useful to flag repetitive sites that are poorly genotyped)

rdratio read-depth ratio of SV carriers to non-carriers (useful for filtering CNVs)

medianrc median coverage 

refratio median REF support for non-carriers

altratio median ALT support for carriers

maxaltratio max. ALT support for carriers

PEsupport total paired end support across all samples

SRsupport total split-read support across all samples

supportsum total depth across all samples

Best, Tobias

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