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GooglingTheCancerGenome / sv-callers

Snakemake-based workflow for detecting structural variants in genomic data
https://research-software.nl/software/sv-callers
Apache License 2.0
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bwa-mem2 + multisample sv-calling and genotyping on non-human genomes #63

Closed arumds closed 1 year ago

arumds commented 3 years ago

Hi,

Does sv-callers allow to detect and genotype SVs across multiple single samples and generate a multi-sample VCF file? If so, what would be the recommended batch size for the number of samples to use in a single analysis?

Moreover, can this be applied on non-human species? and Does it work with BWA-MEM2 aligned BAM files and BWA-MEM2 reference indexes?

We are interested in doing a cohort based SV calling. For this, does sv-caller need all the BAMs in .csv file for SV calling and genotyping SVs? Or does sv-caller allow to call SVs on single BAMs and subsequently allow to genotype across multiple samples?

arnikz commented 3 years ago

Hi,

Does sv-callers allow to detect and genotype SVs across multiple single samples and generate a multi-sample VCF file? If so, what would be the recommended batch size for the number of samples to use in a single analysis?

We are interested in doing a cohort based SV calling. For this, does sv-caller need all the BAMs in .csv file for SV calling and genotyping SVs? Or does sv-caller allow to call SVs on single BAMs and subsequently allow to genotype across multiple samples?

See https://github.com/GooglingTheCancerGenome/sv-callers/issues/51#issuecomment-721025882.

Moreover, can this be applied on non-human species? and Does it work with BWA-MEM2 aligned BAM files and BWA-MEM2 reference indexes?

See #64