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Revision as of 13:44, 9 March 2011
, 13:44, 9 March 2011→Steps
setenv IN /home/hyun/wed/input
setenv IN /home/hyun/wed/input
setenv REF /home/hyun/wed/ref
setenv REF /home/hyun/wed/ref
setenv OUT ~/seq/wednesday/output
setenv OUT ~/seq/wednesday/output
mkdir --p ${OUT}
mkdir --p ${OUT}
9. COMPUTE THE GENOTYPE LIKELIHOOD
9. COMPUTE THE GENOTYPE LIKELIHOOD
${BIN}/samtools-hybrid pileup -g -f ${REF}/human_g1k_v37_chr20.fa ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.glf
${BIN}/samtools-hybrid pileup -g -f ${REF}/human_g1k_v37_chr20.fa ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.glf
${BIN}/samtools-hybrid glfview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.glf | less
${BIN}/samtools-hybrid glfview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.glf | less
10. SINGLE-SAMPLE GENOTYPE CALLING using GLFSINGLE
10. SINGLE-SAMPLE GENOTYPE CALLING using GLFSINGLE
${BIN}/glfSingle --maxDepth 10000 --minMapQuality 20 -p 0.9 -g ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.glf -b ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf
${BIN}/glfSingle --maxDepth 10000 --minMapQuality 20 -p 0.9 -g ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.glf -b ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf
less ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf
less ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf
11. COMPUTE THE GENOTYPE LIKELIHOOD OF HIGH-COVERAGE DATA
11. COMPUTE THE GENOTYPE LIKELIHOOD OF HIGH-COVERAGE DATA
${BIN}/samtools-hybrid pileup -g -f ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.bam > ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.glf
${BIN}/samtools-hybrid pileup -g -f ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.bam > ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.glf
12. SINGLE-SAMPLE GENOTYPE CALLING on the HIGH COVERAGE DATA
12. SINGLE-SAMPLE GENOTYPE CALLING on the HIGH COVERAGE DATA
${BIN}/glfSingle --maxDepth 10000 --minMapQuality 20 -p 0.9 -g ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.glf -b ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf
${BIN}/glfSingle --maxDepth 10000 --minMapQuality 20 -p 0.9 -g ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.glf -b ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf
less ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf
less ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf
13. COUNT NUMBER OF SNPs and OVERLAPS
13. COUNT NUMBER OF SNPs and OVERLAPS
grep -v ^# ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf | wc -l
grep -v ^# ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf | wc -l
grep -v ^# ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | wc -l
grep -v ^# ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | wc -l
cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d | wc -l
cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d | wc -l
cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d
cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d
