Sequence Analysis Practice 2011/03/09: Difference between revisions

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  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}


1. Align using BWA
1. Understanding FASTQ format


${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz.sai
zcat ${IN}/NA12878.exon.sample.read1.fastq.gz | head
zcat ${IN}/NA12878.exon.sample.read2.fastq.gz | head
${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz.sai
zcat ${IN}/NA12878.exon.sample.unpaited.fastq.gz | head
 
${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz > ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz.sai
 
${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz.sai ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.fastq.gz | ${BIN}/samtools-hybrid view -uhS - | ${BIN}/samtools-hybrid sort -m 10000000 - ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.bwa.sorted
 
${BIN}/bwa sampe ${REF}/human_g1k_v37_chr20.fa ${OUT}//NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz.sai ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz.sai ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read1.fastq.gz ${IN}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.read2.fastq.gz | ${BIN}/samtools-hybrid view -uhS - | ${BIN}/samtools-hybrid sort -m 10000000 - ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.paired.bwa.sorted
 
or run
 
sh ${OUT}/sh/step1.sh
 
2. MERGE ALIGNED BAMS INTO A SINGLE BAM
 
${BIN}/samtools-hybrid merge ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.merged.bam ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.paired.bwa.sorted.bam ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.unpaired.bwa.sorted.bam
 
3. BRIEF SUMMARY OF THE BAM
 
${BIN}/samtools-hybrid flagstat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.merged.bam
 
4. MARK DUPLICATED READS
 
${BIN}//superDeDuper -i ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.merged.bam -o ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam -v
 
5. BRIEF SUMMARY OF THE BAM
 
${BIN}/samtools-hybrid flagstat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam


6. VIEW THE ALIGNMENT
press q to quit


${BIN}/samtools-hybrid view  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam | less
2. Align using BWA


TYPE 'q' to finish
  ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \
 
  ${IN}/NA12878.exon.sample.read1.fastq.gz \
7. INDEX THE ALIGNMENT FOR RANDOM ACCESS OF THE BAM
  > ${OUT}/NA12878.exon.sample.read1.fastq.gz.sai
 
  ${BIN}/samtools-hybrid index  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam
 
8. GENOMIC VIEW OF THE ALIGNMENT
 
${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam ${REF}/human_g1k_v37_chr20.fa
 
TYPE 'g' and 20:20000000 (7 consecutive zeros)
 
 
9. QUALITY CHECKING USING QPLOT
 
${BIN}/qplot --plot ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.pdf --stats ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.stats --reference ${REF}/human_g1k_v37_chr20.fa --dbsnp ${REF}/dbsnp.b130.ncbi37.chr20.tbl --gccontent  ${REF}/ncbi37.chr20.gc ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam
   
   
cat ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.stats
  ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \
 
  ${IN}/NA12878.exon.sample.read2.fastq.gz \
The PDF file can be viewed  ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam.qplot.pdf
  > ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai
 
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 glfview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.glf | less
  ${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \
    ${IN}/NA12878.exon.sample.unpaired.fastq.gz \
    > ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai


TYPE 'q' to finish
  ${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa \
 
  ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai \
10. SINGLE-SAMPLE GENOTYPE CALLING using GLFSINGLE
  ${IN}/NA12878.exon.sample.unpaired.fastq.gz \
 
  | ${BIN}/samtools-hybrid view -uhS - \
  ${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}/samtools-hybrid sort -m 10000000 \
  - ${OUT}/NA12878.exon.sample.unpaired.bwa.sorted
   
   
  less ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf
  ${BIN}/bwa sampe ${REF}/human_g1k_v37_chr20.fa \
  ${OUT}//NA12878.exon.sample.read1.fastq.gz.sai \
  ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai \
  ${IN}/NA12878.exon.sample.read1.fastq.gz \
  ${IN}/NA12878.exon.sample.read2.fastq.gz \
  | ${BIN}/samtools-hybrid view -uhS - \
  | ${BIN}/samtools-hybrid sort -m 10000000 \
  - ${OUT}/NA12878.exon.sample.paired.bwa.sorted


TYPE 'q' to finish
3. Merge multiple BAMs into one
${BIN}/samtools-hybrid merge ${OUT}/NA12878.exon.sample.merged.bam \
  ${OUT}/NA12878.exon.sample.paired.bwa.sorted.bam  \
  ${OUT}/NA12878.exon.sample.unpaired.bwa.sorted.bam


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
4. View SAM/BAM format
  ${BIN}/samtools-hybrid view -h ${OUT}/NA12878.exon.sample.merged.bam | head -5


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
5. Mark Deuplicate Reads
  ${BIN}/superDeDuper -i ${OUT}/NA12878.exon.sample.merged.bam \
less ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf
  -o ${OUT}/NA12878.exon.sample.deduped.bam -v
 
TYPE 'q' to finish
 
13. COUNT NUMBER OF SNPs and OVERLAPS


grep -v ^# ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.vcf | wc -l
6. Visualize alignment to reference genome
  ${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon.sample.deduped.bam \
grep -v ^# ${OUT}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf | wc -l
    ${REF}/human_g1k_v37_chr20.fa
 
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
  ${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.deduped.bam ${REF}/human_g1k_v37_chr20.fa
TYPE g , and  20:19989392
TYPE g, and  20:20032998
 
${BIN}/samtools-hybrid tview ${IN}/NA12878.high_coverage.ILLUMINA.chr20.19986kb-20281kb.bam ${REF}/human_g1k_v37_chr20.fa
 
TYPE g , and  20:19989392
TYPE g, and  20:20032998
 
14. SUMMARIZE STATISTICS
 
perl ${BIN}/vcfSummary.pl --vcf ${OUT}/NA12878.exon-targetted.ILLUMINA.chr20.19986kb-20281kb.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.high_coverage.ILLUMINA.chr20.19986kb-20281kb.vcf --dbsnp ${REF}/dbsnp_129_b37.rod.chr20.map --bfile ${REF}/hapmap3_r3_b37_fwd.consensus.qc.poly.chr20

Revision as of 17:07, 9 March 2011

Overview

Below lists a sequence of practice mapping fastq files to bam files, performing variant calling and variout quality checks.

Steps

0. SETTING UP ENVIRONMENTAL VARIABLES 

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

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

1. Understanding FASTQ format

zcat ${IN}/NA12878.exon.sample.read1.fastq.gz | head zcat ${IN}/NA12878.exon.sample.read2.fastq.gz | head zcat ${IN}/NA12878.exon.sample.unpaited.fastq.gz | head

press q to quit

2. Align using BWA 

${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \
  ${IN}/NA12878.exon.sample.read1.fastq.gz \
 > ${OUT}/NA12878.exon.sample.read1.fastq.gz.sai

${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \
  ${IN}/NA12878.exon.sample.read2.fastq.gz \
  > ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai

${BIN}/bwa aln -q 15 ${REF}/human_g1k_v37_chr20.fa \
   ${IN}/NA12878.exon.sample.unpaired.fastq.gz \
   > ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai

${BIN}/bwa samse ${REF}/human_g1k_v37_chr20.fa \
  ${OUT}/NA12878.exon.sample.unpaired.fastq.gz.sai \ 
  ${IN}/NA12878.exon.sample.unpaired.fastq.gz \
  | ${BIN}/samtools-hybrid view -uhS - \
 | ${BIN}/samtools-hybrid sort -m 10000000 \
 - ${OUT}/NA12878.exon.sample.unpaired.bwa.sorted

${BIN}/bwa sampe ${REF}/human_g1k_v37_chr20.fa \
 ${OUT}//NA12878.exon.sample.read1.fastq.gz.sai \
 ${OUT}/NA12878.exon.sample.read2.fastq.gz.sai \
 ${IN}/NA12878.exon.sample.read1.fastq.gz \
 ${IN}/NA12878.exon.sample.read2.fastq.gz \
 | ${BIN}/samtools-hybrid view -uhS - \
 | ${BIN}/samtools-hybrid sort -m 10000000 \
 - ${OUT}/NA12878.exon.sample.paired.bwa.sorted

3. Merge multiple BAMs into one 

${BIN}/samtools-hybrid merge ${OUT}/NA12878.exon.sample.merged.bam \
  ${OUT}/NA12878.exon.sample.paired.bwa.sorted.bam  \
  ${OUT}/NA12878.exon.sample.unpaired.bwa.sorted.bam


4. View SAM/BAM format 

${BIN}/samtools-hybrid view -h ${OUT}/NA12878.exon.sample.merged.bam | head -5


5. Mark Deuplicate Reads 

${BIN}/superDeDuper -i ${OUT}/NA12878.exon.sample.merged.bam \
 -o ${OUT}/NA12878.exon.sample.deduped.bam -v

6. Visualize alignment to reference genome 

${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon.sample.deduped.bam \
   ${REF}/human_g1k_v37_chr20.fa
Retrieved from "http://genome.sph.umich.edu/w/index.php?title=Sequence_Analysis_Practice_2011/03/09&oldid=3043"