Tutorial: EMMAX GotCloud STOM: Lecture 6

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STOM 2014 Workshop - Practical Sessions 6

Lecture 6

The slides describing the notes below are available here (PDF)

Basic Setup

If you still have the logged in console from lecture 5 practical session, you may skip this part

  • To see the files for the session 5(,6, and 8), type
ls /data/stom2014/session5/

If you see any errors, please let me know now!

  • For convenience, let’s set some variables
export S5=/data/stom2014/session5
  • And check the input files
ls $S5/examples/bams

Preparing Input Files

  • Index file - See the example index file already prepared for this project
less $S5/examples/index/chr7.CFTR.low_coverage.index
  • Configuration File - See the example configuration file below.
cat $S5/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

Default options should be mostly fine in many other cases. In this example, because it is not genome-wide calling, reference files are modified to be chr7-specific

Run GotCloud SNP calling Pipeline

  • Using the prepared input files, call SNPs using the gotcloud SNP calling pipeline

(WARNING: This step will take a long time, up to 5 minutes, because it processes nearly 100 BAMs, 4 jobs simultaneously at a time)

time $S5/gotcloud/gotcloud snpcall --conf $S5/examples/index/chr7.CFTR.low_coverage.conf --outDir ~/out/snps --baseprefix $S5/examples --region 7:117000000-117500000 --numjobs 4
  • Check the summary statistics of SNP call to evaluate its quality
cat ~/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary

Running LD-aware genotype refinement

(WARNING: This step will take a long time, up to 2 minutes)

time $S5/gotcloud/gotcloud beagle --conf $S5/examples/index/chr7.CFTR.low_coverage.conf --outDir ~/out/snps --baseprefix $S5/examples  --region 7:117000000-117500000 --numjobs 2

Understanding the Output Files

  • To see the content of VCF file, try
zless ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz
  • If you want to look at a variant at a particular genomic position or in a particular genomic region, use the tabix utility to facilitate random access without reading the whole VCF file.
$S5/epacts/bin/tabix ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz 7:117149147-117149147
The example above displays known CFTR risk variant, R75Q

Using samtools to visualize the sequence reads and verify the variant calls

samtools tview $S5/examples/bams/NA12843.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam $S5/examples/chr7Ref/hs37d5.chr7.fa

After running this.. try to

  1. Type 'g'
  2. Type '7:117149147'
  3. Type 'n' to change the display (color by nucleotide)
  4. Move with left arrow to see the variant site clearly