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

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.

vcf software sv • 2.9k views
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9.5 years ago
Rm 8.2k

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

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7.6 years ago
Ming Tang ★ 2.9k

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

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