Hmkang: /* Steps */

2011-03-10T06:14:31Z

Steps

← Older revision		Revision as of 02:14, 10 March 2011
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	${BIN}/samtools-hybrid tview ${IN}/NA12878.highcov.sample.bam ${REF}/human_g1k_v37_chr20.fa		${BIN}/samtools-hybrid tview ${IN}/NA12878.highcov.sample.bam ${REF}/human_g1k_v37_chr20.fa
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	11. SUMMARIZE VCF STATISTICS		11. SUMMARIZE VCF STATISTICS

Hmkang: Created page with '== Overview == The aim for today's practice is to perform variant calling from sequence alignment files == Steps == 0. SETTING UP ENVIRONMENTAL VARIABLES setenv BIN /home/hy…'

2011-03-10T05:58:38Z

Created page with '== Overview == The aim for today's practice is to perform variant calling from sequence alignment files == Steps == 0. SETTING UP ENVIRONMENTAL VARIABLES setenv BIN /home/hy…'

New page

== Overview ==

The aim for today's practice is to perform variant calling from sequence alignment files

== Steps ==

0. SETTING UP ENVIRONMENTAL VARIABLES

setenv BIN /home/hyun/thu/bin
setenv IN /home/hyun/thu/input
setenv REF /home/hyun/thu/ref

setenv OUT ~/seq/thursday/output
mkdir --p ${OUT}

1. EXON-TARGETTED DATA : COMPUTING GENOTYPE LIKELHOOD FROM BAM FILES

${BIN}/samtools-hybrid pileup -g -f ${REF}/human_g1k_v37_chr20.fa ${OUT}/NA12878.exon.sample.deduped.bam > ${OUT}/NA12878.exon.sample.glf

2. EXON-TARGETTED DATA : VIEW THE GENOTYPE LIKELIHOOD FORMAT

${BIN}/samtools-hybrid glfview ${OUT}/NA12878.exon.sample.glf | less

TYPE 'q' to finish

3. EXON-TARGETTED DATA : SINGLE-SAMPLE GENOTYPE CALLING using GLFSINGLE

${BIN}/glfSingle --maxDepth 10000 --minMapQuality 20 -p 0.9 -g ${OUT}/NA12878.exon.sample.glf -b ${OUT}/NA12878.exon.sample.vcf

4. EXON-TARGETTED DATA : VIEW THE VCF FILES AND COUNT # OF SNPS

less ${OUT}/NA12878.exon.sample.vcf

grep -v ^# ${OUT}/NA12878.exon.sample.vcf | wc -l

5. DEEP-COVERAGE GENOME : COMPUTE THE GENOTYPE LIKELIHOOD

${BIN}/samtools-hybrid pileup -g -f ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.highcov.sample.bam > ${OUT}/NA12878.highcov.sample.glf

6. DEEP-COVERAGE GENOME : SINGLE-SAMPLE VARIANT CALLING

${BIN}/glfSingle --maxDepth 10000 --minMapQuality 20 -p 0.9 -g ${OUT}/NA12878.highcov.sample.glf -b ${OUT}/NA12878.highcov.sample.vcf

7. DEEP-COVERAGE GENOME : VIEW THE VCF FILES AND COUNT # OF SNPS

less ${OUT}/NA12878.highcov.sample.vcf

8. VIEW THE VCF FILES AND COUNT # OF SNPS

grep -v ^# ${OUT}/NA12878.highcov.sample.vcf | wc -l

9. EVALUATE OVERLAP BETWEEN THE TWO SETS OF VARIANT CALLS

cat ${OUT}/NA12878.exon.sample.vcf ${OUT}/NA12878.highcov.sample.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d | wc -l

cat ${OUT}/NA12878.exon.sample.vcf ${OUT}/NA12878.highcov.sample.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d

10. VIEW ACTUAL ALIGNMENT AT SNP POSITIONS

${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon.sample.deduped.bam ${REF}/human_g1k_v37_chr20.fa

TYPE g, and 20:19989392
TYPE g, and 20:20032998

${BIN}/samtools-hybrid tview ${IN}/NA12878.highcov.sample.bam ${REF}/human_g1k_v37_chr20.fa

TYPE g, and 20:19989392
TYPE g, and 20:20032998

11. SUMMARIZE VCF STATISTICS

perl ${BIN}/vcfSummary.pl --vcf ${OUT}/NA12878.exon.sample.vcf --dbsnp ${REF}/dbsnp_129_b37.rod.chr20.map --bfile ${REF}/hapmap3_r3_b37_fwd.consensus.qc.poly.chr20

perl ${BIN}/vcfSummary.pl --vcf ${OUT}/NA12878.highcov.sample.vcf --dbsnp ${REF}/dbsnp_129_b37.rod.chr20.map --bfile ${REF}/hapmap3_r3_b37_fwd.consensus.qc.poly.chr20

Editing Sequence Analysis Practice 2011/03/10 - Revision history

Hmkang: /* Steps */

Hmkang: Created page with '== Overview == The aim for today's practice is to perform variant calling from sequence alignment files == Steps == 0. SETTING UP ENVIRONMENTAL VARIABLES setenv BIN /home/hy…'