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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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vcf format for SV #148

Open poojachandra opened 2 months ago

poojachandra commented 2 months ago

Hi, I am trying to give vcf file as input for SV generated from Svaba, Manta and Gridds but getting an error 'VCF appears to contain multiple samples or non-standard fields. Please provide a single-sample VCF with appropriate formatting'.

Is there a way to fix this issue ? The vcf file format is correct. Is there a sample vcf for SV that I could perhaps use as an example ?

Thanks

jluebeck commented 2 months ago

Hi, thanks for checking in about this. It is very hard to say without seeing the VCF itself. By and chance could you share the VCF to jluebeck@ucsd.edu? If not possible to share the whole VCF, can you share part of it - say the first hundred entries?

Thank you! Jens