1,120
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→STEP 3 : Run GotCloud SNP Calling Pipeline
...
...
To run SNP calling pipeline, we need to prepare index file corresponding to the BAM files with sample IDs
% cat ${GC}/examples/index/chr7.CFTR.low_coverage.index
% cat ${GC}/examples/index/chr7.CFTR.low_coverage.index
NA06984 EUR bams/NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
NA06984 EUR bams/NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
...
...
Also, we need a configuration file.
% cat ${GC}/examples/index/chr7.CFTR.low_coverage.conf
% cat ${GC}/examples/index/chr7.CFTR.low_coverage.conf
HM3_VCF = $(REF_ROOT)/hapmap_3.3.b37.sites.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
OMNI_VCF = $(REF_ROOT)/1000G_omni2.5.b37.sites.PASS.chr7.CFTR.vcf.gz
Then we're ready to run SNP calling pipeline
% ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
% ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
CHRS = 7
CHRS = 7
BAM_INDEX = index/chr7.CFTR.low_coverage.index
BAM_INDEX = index/chr7.CFTR.low_coverage.index
Commands finished in 306 secs with no errors reported
Commands finished in 306 secs with no errors reported
--------------------------------------------------------------------
--------------------------------------------------------------------
We can summarize the quality of variants.
% cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
% cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------
To run LD-refinement you can run beagle only (gotcloud beagle) or beagle+thunder (gotcloud ldrefine) to improve the quality of genotypes.
If you're interested in looking at individual reads from the variant, samtools tview provides a good alternative to IGV. In order to see CFTR R75Q variant in one of the variant carriers, you can run
% samtools tview ${GC}/examples/bams/NA12843.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam ${GC}/examples/chr7Ref/hs37d5.chr7.fa
% samtools tview ${GC}/examples/bams/NA12843.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam ${GC}/examples/chr7Ref/hs37d5.chr7.fa
And follow the steps
* Type ‘g’
* Type 7:117149147
* Type ‘n’ to color by nucleotide
* Move with left arrow to see the variant site clearly
% ${GC}/gotcloud/gotcloud beagle --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
Key configurations:
GOTCLOUD_ROOT: /home/presenter02/day2/session1/uwcmg_2013_08/gotcloud
OUT_DIR: snps
BAM_INDEX: index/chr7.CFTR.low_coverage.index
REF: chr7Ref/hs37d5.chr7.fa
CHRS: 7
BATCH_TYPE: local
BATCH_OPTS:
Processing the following steps...
9: RUN_BEAGLE
10: RUN_SUBSET
Call region is 7:117000000-117500000
Generating commands for chr7...
--------------------------------------------------------------------
Finished creating makefile /home/presenter02/test/snps/umake.Makefile
Running /home/presenter02/test/snps/umake.Makefile
Commands finished in 74 secs with no errors reported
--------------------------------------------------------------------
== STEP 4 : EPACTS association analysis ==
== STEP 4 : EPACTS association analysis ==
