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Revision as of 14:36, 13 November 2014
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'''Note:''' the latest version of this practical is available at: [[SeqShop: Variant Calling and Filtering for INDELs Practical]]
* The ones here is the original one from the June workshop (updated to be run from elsewhere)
== Goals of This Session ==
== Goals of This Session ==
* What we want to learn
* What we want to learn
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This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]]
This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, June 2014|Alignment Tutorial]]
It also uses the bam.index file created in the SnpCall Tutorial. If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#GotCloud_BAM_Index_File|GotCloud BAM Index File]]
It also uses the bam.index file created in the SnpCall Tutorial. If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical, June 2014#GotCloud_BAM_Index_File|GotCloud BAM Index File]]
* BAMs->INDELs rather than BAMs->SNPs
* BAMs->INDELs rather than BAMs->SNPs
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]]
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, June 2014#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]]
== Running GotCloud Indel ==
== Running GotCloud Indel ==
Edit indel.reference.txt and specify the correct path to ${SS}
Edit indel.reference.txt and specify the correct path to ${SS}
nedit ${OUT}/indel.reference.txt
nedit ${OUT}/indel.reference.txt
*'''Replace all occurrences of /home/mktrost/ with the path to your seqshop directory.'''
*'''Replace all occurrences of <code>username</code> with your username (or the correct path to your seqshop example directory).'''
*:[[File:IndelRef.png]]
${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
