Created
February 17, 2018 15:33
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SV-Plaudit how to commands
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| git clone --recursive https://github.com/jbelyeu/SV-plaudit.git | |
| cd SV-plaudit | |
| samtools view -b ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/NA12892/high_coverage_alignment/NA12892.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam 22 > NA12892.22.bam | |
| samtools view -b ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/NA12891/high_coverage_alignment/NA12891.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam 22 > NA12891.22.bam | |
| samtools view -b ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/NA12878/high_coverage_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam 22 > NA12878.22.bam | |
| samtools index NA12878.22.bam | |
| samtools index NA12891.22.bam | |
| samtools index NA12892.22.bam | |
| bcftools view -c 1 -s NA12878 ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/integrated_sv_map/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz > NA12878.22.vcf | |
| mkdir sv_imgs | |
| Samplot/src/samplot_vcf.sh -S Samplot/src/samplot.py -o sv_imgs -v NA12878.22.vcf NA12878.22.bam NA12891.22.bam NA12892.22.bam | |
| python PlotCritic/setup.py -p NA12878_trio_22 -e ryan@layerlab.org -a YOUR_AWS_ACCESS_KEY_ID -s "YOUR_AWS_SECRET_ACCESS_KEY" | |
| python upload.py -d sv_imgs -c PlotCritic/config.json | |
| python PlotCritic/retrieval.py -c PlotCritic/config.json > retrieved_data.csv | |
| python annotate.py -s retrieved_data.mod.csv -v NA12878.22.vcf -a NA12878.22.score.vcf -o mean -n 1,0,1 |
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