SVgoback

SV calling initiated from the GOBACK project, but become a general pipeline on HGSC cluster

Caller

Further filter by excluding RLCR region. ITX and CTX are in pgl format, the others are in bed format.

breakdancer

• Calls: DEL INS INV ITX CTX
• SVtyper genotyped (Does not genotype ITX CTX INS)
• Simple filter: for DEL INV, based on SVtyper, genotype 0/1 or 1/1, and QUAL>1; for INS ITX CTX, require DP > 10

1. breakdancer_call.sub
2. breakdancer_svtyper.sub
3. breakdancer_categorize.sub

cnvnator

• Calls: DEL DUP (also CNV based on read-depth)
• Use its own genotyper
• No simple filter applied

1. cnvnator_call.sub
2. cnvnator_categorize.sub

delly

• Calls: DEL DUP (tandem only, also CNV based on read-depth) INV CTX (as BND)
• Use its own genotyper
• Simple filter: based on genotype 0/1 or 1/1, and PASS for the site and for the sample

1. delly_call.sub
2. delly_categorize.sub

lumpy

• Calls: DEL DUP (tandem only) INV ITX (as BND) CTX (as BND)
• SVtyper genotyped
• Filter: based on SVtyper, genotype 0/1 or 1/1, and QUAL>1. Also only keep one record for ITX and CTX

1. lumpy_preprocess.sub
2. lumpy_call.sub
3. lumpy_svtyper.sub
4. lumpy_categorize.sub

manta

• Calls: DEL DUP (tandem only) INS INV CTX (as BND)
• Use its own genotyper
• Filter: PASS for the site and for the sample. Also only keep one record for CTX

1. manta_call.sub
2. manta_categorize.sub

tiddit

• Calls: DEP DUP (both disparse and tandem, also CNV based on read-depth) INV ITX (as BND) CTX (as BND)
• Use its own genotyper
• Filter: PASS for the site. Combine disparse and tandem duplications.

1. tiddit_call.sub
2. tiddit_categorize.sub

Event

DEL DUP INS INV

Further filter by limiting the size within (100bp,1Mb). And remove calls overlapping with RLCRs_no_Repeat_Masker.txt

DEL

• breakdancer
• cnvnator
• delly
• lumpy
• manta
• tiddit

DUP (both disparse and tandem)

• cnvnator
• delly
• lumpy
• manta
• tiddit

INV

• breakdancer
• delly
• lumpy
• manta
• tiddit

INS

• breakdancer
• manta

ITX CTX

Remove calls overlapping with RLCRs_no_Repeat_Masker.txt

Output is in pgl format

ITX

• breakdancer
• delly
• lumpy
• manta
• tiddit

CTX

• breakdancer
• delly
• lumpy
• manta
• tiddit

CNV

• cnvnator
• delly
• tiddit

Inheritance

Private

• The SV does not exist in any other samples
• TODO: confirm using genotyping

Family specific

• The SV overlap with at least one other family member, but not other samples outside the family
• TODO: confirm using genotyping

Denovo candidate for proband

• The SV does not exist in any healthy controls. (Only run for probands, different between Private is whether in other probands or not)
• TODO: confirm using genotyping

Recessive candidate for proband

From family specific SV, genotyping to select SV that are 1/1 in proband, 0/1 in parents, and not 1/1 in sibling

• TODO: extend the genotyping candidate to family-specific SV found in all family members

Compound het candidate for proband

TODO later