intragenic-rearrangement-burden

Calculation of intragenic rearrangement burden based on structural variant calling files

vcf file specifications

Required: vcf file must be in GRCh37 genome build.
Required: vcf file must contain the following columns #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOUR.
Required: vcf file ALT column must contain rearrangement annotation like "A]1:193674914]".
Required: vcf file must contain "PASS" in the FILTER column.

usage for CountIGRBurden.exe

Users need to type in four arguments for the CountIGRBurden.exe to run the calculation:

1. input vcf file match the specified format above;
2. sample name
3. output IGR count file
4. exon database provided with this package (UCSCAndGencodeCompV27lift37.annotation.gtf.exon_intron.merge.an)

./CountIGRBurden.exe input.vcf sample_name output exondb

Example

./CountIGRBurden.exe example.sv.vcf example example.IGRcount.tsv UCSCAndGencodeCompV27lift37.annotation.gtf.exon_intron.merge.an

Example Output

SampleID	Intergenic.AGR(n)	Intergenic.Inter-chr(n)	Intergenic.Intro-chr(n)	Intragenic.DEL(n)	Intragenic.DUP(n)	IGR.count(DUP+DEL)	IGR.burden(sqrt)
example	1	74	6	8	113	121	11

Notes to headers:
Intergenic.AGR(n): adjacent intergenic rearrangements.
Intergenic.Inter-chr(n): interchrosomal intergenic rearrangements.
Intergenic.Intro-chr(n): intrachrosomal intergenic rearrangements.
Intragenic.DEL(n): intragenic deletion counts.
Intragenic.DUP(n): intragenic duplication counts.
IGR.count(DUP+DEL): IGR counts including intragenic duplications and deletions
IGR.burden(sqrt): square root transformed IGR counts.