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% cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
% cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
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FILTER #SNPs #dbSNP %dbSNP %CpG %CpG %Known %Novel %nCpG-K %nCpG-N %HM3 %HM3
FILTER #SNPs #dbSNP %dbSNP %CpG %CpG %Known %Novel %nCpG-K %nCpG-N %HM3 %HM3
% time ${GC}/gotcloud/gotcloud beagle --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
% ${GC}/gotcloud/gotcloud beagle --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
% samtools tview ${GC}/examples/bams/NA12843.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam ${GC}/examples/chr7Ref/hs37d5.chr7.fa
% samtools tview ${GC}/examples/bams/NA12843.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam ${GC}/examples/chr7Ref/hs37d5.chr7.fa
