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% ls ${GC}/examples/bams
% ls ${GC}/examples/bams
NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam NA12272.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam.bai
NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam.bai NA12273.mapped.ILLUMINA.bwa.CEU.low_coverage.20121211.CFTR.bam
NA06985.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam NA12273.mapped.ILLUMINA.bwa.CEU.low_coverage.20121211.CFTR.bam.bai
NA06985.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam.bai NA12275.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
NA06986.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam NA12275.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam.bai
NA06986.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam.bai NA12282.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam
NA06989.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam NA12282.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam.bai
NA06989.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam.bai NA12283.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam
NA06994.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam NA12283.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam.bai
NA06994.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam.bai NA12286.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam
NA07000.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam NA12286.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam.bai
NA07000.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam.bai NA12287.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam
NA07037.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.CFTR.bam NA12287.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam.bai
...
% cat ${GC}/examples/index/chr7.CFTR.low_coverage.index
% cat ${GC}/examples/index/chr7.CFTR.low_coverage.index
NA06984 EUR bams/NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
NA06985 EUR bams/NA06985.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
NA06986 EUR bams/NA06986.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam
NA06989 EUR bams/NA06989.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
NA06994 EUR bams/NA06994.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
NA07000 EUR bams/NA07000.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam
NA07037 EUR bams/NA07037.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.CFTR.bam
NA07048 EUR bams/NA07048.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
NA07051 EUR bams/NA07051.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
NA07056 EUR bams/NA07056.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam
...
% cat ${GC}/examples/index/chr7.CFTR.low_coverage.conf
% cat ${GC}/examples/index/chr7.CFTR.low_coverage.conf
CHRS = 7
BAM_INDEX = index/chr7.CFTR.low_coverage.index
############
# References
REF_ROOT = chr7Ref
#
REF = $(REF_ROOT)/hs37d5.chr7.fa
INDEL_PREFIX = $(REF_ROOT)/1kg.pilot_release.merged.indels.sites.hg19
DBSNP_VCF = $(REF_ROOT)/dbsnp_135.b37.chr7.CFTR.vcf.gz
HM3_VCF = $(REF_ROOT)/hapmap_3.3.b37.sites.chr7.CFTR.vcf.gz
OMNI_VCF = $(REF_ROOT)/1000G_omni2.5.b37.sites.PASS.chr7.CFTR.vcf.gz
% time ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
% ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
% cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
% cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
--------------------------------------------------------------------------------------------------------------
FILTER #SNPs #dbSNP %dbSNP %CpG %CpG %Known %Novel %nCpG-K %nCpG-N %HM3 %HM3
Known Novel Ts/Tv Ts/Tv Ts/Tv Ts/Tv sens /SNP
--------------------------------------------------------------------------------------------------------------
INDEL5 11 8 72.7 25.0 0.0 3.00 0.50 2.00 0.50 0.000 0.000
INDEL5;SVM 8 4 50.0 50.0 25.0 0.33 0.33 1.00 0.00 0.000 0.000
PASS 1388 1186 85.4 15.5 11.4 2.10 1.62 1.79 1.42 85.083 11.095
SVM 131 33 25.2 9.1 9.2 1.06 0.85 0.88 0.78 0.000 0.000
--------------------------------------------------------------------------------------------------------------
FILTER #SNPs #dbSNP %dbSNP %CpG %CpG %Known %Novel %nCpG-K %nCpG-N %HM3 %HM3
Known Novel Ts/Tv Ts/Tv Ts/Tv Ts/Tv sens /SNP
--------------------------------------------------------------------------------------------------------------
INDEL5 19 12 63.2 33.3 14.3 1.40 0.40 1.67 0.20 0.000 0.000
PASS 1388 1186 85.4 15.5 11.4 2.10 1.62 1.79 1.42 85.083 11.095
SVM 139 37 26.6 13.5 9.8 0.95 0.82 0.88 0.74 0.000 0.000
--------------------------------------------------------------------------------------------------------------
PASS 1388 1186 85.4 15.5 11.4 2.10 1.62 1.79 1.42 85.083 11.095
FAIL 150 45 30.0 15.6 9.5 1.14 0.81 1.00 0.73 0.000 0.000
TOTAL 1538 1231 80.0 15.5 10.7 2.05 1.27 1.75 1.12 85.083 10.013
------------------------------------------------------------------------------------------------------------
% 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
% 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
