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SeqShop: Analysis of Structural Variation Practical, June 2014 (view source)

Revision as of 14:46, 17 June 2014

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''(WARNING: Under Construction)''
 
''(WARNING: Under Construction)''
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==Introduction==
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See the [[Media:SeqShop - GotCloud svcall.pdf|introductory slides]] for an intro to this tutorial.
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== Goals of This Session ==
 
== Goals of This Session ==
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This is the same setup you did for the previous tutorial, but you need to redo it each time you log in. It will setup some environment variables to point you to:
 
This is the same setup you did for the previous tutorial, but you need to redo it each time you log in. It will setup some environment variables to point you to:
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* GotCloud program
 
* GotCloud program
 
* Tutorial input files
 
* Tutorial input files
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== Examining GotCloud/GenomeSTRiP Input files ==
 
== Examining GotCloud/GenomeSTRiP Input files ==
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=== Sequnce Alignment Files: BAM Files ===
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=== Sequnce Alignment Files: BAM Files and Index Files===
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Per sample BAM files contain sequence reads that are mapped to positions in the genome.
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The GotCloud Indel caller takes the same inputs as GotCloud snpcall.
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* BAMs->SVs rather than BAMs->SNPs
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For a reminder on how to look at/read BAM files, see: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#BAM_Files|SeqShop Aligment: BAM Files]]
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For this tutorial, we will use the 4 BAMs produced in the [[SeqShop: Sequence Mapping and Assembly Practical]] as well as with 58 BAMs that were pre-aligned to that 1MB region of chromosome 22.
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If you want a reminder, of what they look like, here is a link to the previous tutorial : [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]]
    
=== Reference Files ===
 
=== Reference Files ===
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* See [[GotCloud: Genetic Reference and Resource Files]] for more information on downloading/generating reference files
 
* See [[GotCloud: Genetic Reference and Resource Files]] for more information on downloading/generating reference files
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For GotCloud/GenomeSTRiP, you need:
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Similar to SNP and Indel calling, you need
 
# Reference genome FASTA file
 
# Reference genome FASTA file
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For running GenomeSTRiP, you additionally need:
 
# Masked FASTA file to exclude hard-to-align regions
 
# Masked FASTA file to exclude hard-to-align regions
 
# PloidyMap file indicating the regions of genomes with unusual ploidy (e.g. chrX, chrY)
 
# PloidyMap file indicating the regions of genomes with unusual ploidy (e.g. chrX, chrY)
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</div>
 
</div>
 
</ul>
 
</ul>
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ls $REF
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<ul>
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<div class="mw-collapsible mw-collapsed" style="width:200px">
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<li>View Results</li>
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<div class="mw-collapsible-content">
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1000G_omni2.5.b37.sites.PASS.chr22.vcf.gz            hapmap_3.3.b37.sites.chr22.vcf.gz.tbi  human.g1k.v37.chr22.fa.bwt
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1000G_omni2.5.b37.sites.PASS.chr22.vcf.gz.tbi        human.g1k.v37.chr22-bs.umfa            human.g1k.v37.chr22.fa.fai
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1kg.pilot_release.merged.indels.sites.hg19.chr22.vcf  human.g1k.v37.chr22.dict              human.g1k.v37.chr22.fa.pac
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dbsnp_135.b37.chr22.vcf.gz                            human.g1k.v37.chr22.fa                human.g1k.v37.chr22.fa.sa
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dbsnp_135.b37.chr22.vcf.gz.tbi                        human.g1k.v37.chr22.fa.amb            human.g1k.v37.chr22.winsize100.gc
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hapmap_3.3.b37.sites.chr22.vcf.gz                    human.g1k.v37.chr22.fa.ann
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</div>
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</div>
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</ul>
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Additional reference and parameters
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ls $SV/ref
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human_g1k_v37.chr22.mask.100.fasta  human_g1k_v37.chr22.mask.100.fasta.dict  human_g1k_v37.chr22.mask.100.fasta.fai
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ls $SV/conf
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genstrip_parameters.txt  humgen_g1k_v37_ploidy.chr22.map  humgen_g1k_v37_ploidy.map
    
=== GotCloud BAM Index File ===
 
=== GotCloud BAM Index File ===
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/10861"

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