View source for Editing Sequence Analysis Practice 2011/03/10

== 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