Programs That Report Structural Variations For Tumor/Normal In Vcf Format

Question

[14134125465346445]

What software is available out there that will read in one or several BAM files and report SV events, including copy-number changes and allelic imbalances, in vcf 4.1 format? For example, for pairs of tumor/normal bam files, but alternatively, also software that will report SVs for single somatic bam files against the genome reference.

Answer 1

[Rm]

As far as I know most SV tools does not report the out puts to VCF format. You need to write a script to convert them to VCF.

See the SV VCF format here

Answer 2

[Ming Tommy Tang]

lumpy outputs vcf file https://github.com/arq5x/lumpy-sv