How do I connect the input and output of the three software (manta+svimmer+graphtyper)

[koujiaodahan]

Hi Manta has three variants file:diploidSV.vcf.gz ,candidateSV.vcf.gz and candidateSmallIndels.vcf.gz so ,should i merge the corresponding which file type(candidateSV.vcf.gz ? discard diploidSV.vcf.gz andcandidateSmallIndels.vcf.gz) to the config.sh of make_graphtyper_pipeline.sh? In addition, the make_graphtyper_pipeline.sh is suitable for connecting to manta+svimmer to run genotype ? can you give me a example of config.sh and running make_graphtyper_pipeline.sh ?

Thanks ,Looking forward to your reply!

[hannespetur]

I recommend using diploidSV.vcf.gz

I no longer recommend using make_graphtyper_[sv_]pipeline.sh scripts and instead use the genotype subcommand for SNP/indel genotyping and genotype_sv for SV calling.

Best, Hannes