Daniel:Notebook/Haplotyping/2014-7-15
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Microfluidic Data Processing
The microfluidic data from Eric will need processing, similar to the processing done on the BAC pools. This will eliminate strand overhangs and help to improve the phasing for the microfluidic data. I'll be using Athurva's pipeline on genome miner for this. I may change to TSCC if the allocation is large.
Workflow
Trying out a single index, index09 from HL163 right now.
- The sequencing files are /media/Syn_15T/Eric_15T/HL163/CoRE/s_1_1_Indx09.txt and /media/Syn_15T/Eric_15T/HL163/CoRE/s_4_1_Indx09.txt
- The folder I am putting these in to is /media/LTS_15T/DEJ_LTS/microfluidics_data, in the test_Indx09 folder
- Run Athurva's BWA/GATK pipeline
- /home/ajgore/AG_Ext12T/GATK_01022012/variantCallerBwaGATK-latest/variantCallerBwaGATK.pl test_Indx09_coRE_HL163.info > test_Indx09_coRE_HL163.status &