We applied SVelter to YRI trio first, then we validated our call sets using pacbio long sequences, and analyzed the common and unique SVs.
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Run SVelter setup, NullModel, BPSearch on YRI trio
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Integrate breakpoints from each sample by running:
BP.Merge.Multi.Sample.py --chromosome chr1 --workdir /scratch/remills_flux/xuefzhao/SV_discovery_index/download/ --reference /scratch/remills_flux/xuefzhao/reference/GRCh38.1KGP/GRCh38_full_analysis_set_plus_decoy_hla.fa
3.Run SVelter SVPredict, SVIntegrate on TRI trio
Pacbio.Validator.py vcf --sv-input /scratch/remills_flux/xuefzhao/SV_discovery_index/download/SVelter.CommonBPs/NA19240.Common.BPs.vcf --output-path /scratch/remills_flux/xuefzhao/SV_discovery_index/download/SVelter.CommonBPs/NA19240.vcf.PacbioValidation --pacbio-input /scratch/remills_flux/xuefzhao/SV_discovery_index/smrt.download/alignment/NA19240.XXX.bam --reference /scratch/remills_flux/xuefzhao/reference/GRCh38.1KGP/GRCh38_full_analysis_set_plus_decoy_hla.fa
SV.Merge.Multi.Sample.py vcf --workdir /scratch/remills_flux/xuefzhao/SV_discovery_index/download/SVelter.CommonBPs
SV.Merge.Multi.Sample.py svelter --workdir /scratch/remills_flux/xuefzhao/SV_discovery_index/download/SVelter.CommonBPs
SV.PacVal.file.filter.py --input /scratch/remills_flux/xuefzhao/SV_discovery_index/download/SVelter.CommonBPs/Common.SVs.samples.minus.0.PacVal --score-cff 0.2 --PB-score-pos 11
SV.PacVal.file.filter.py --input /scratch/remills_flux/xuefzhao/SV_discovery_index/download/SVelter.CommonBPs/Common.SVs.samples.minus.1.PacVal --score-cff 0.2 --PB-score-pos 11
SV.PacVal.file.filter.py --input /scratch/remills_flux/xuefzhao/SV_discovery_index/download/SVelter.CommonBPs/Common.SVs.samples.minus.2.PacVal --score-cff 0.2 --PB-score-pos 11