Daniel:Notebook/Haplotyping/2014-8-22

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Microfluidics Data[edit]

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After much playing around with the errors, I've decided to scrap the variant recalibration. I noticed that Athurva's pipeline uses a particularly old version of GATK, version 1.x (they are on 3.x now). So I downloaded the new .jar file, and I'm going to run the Haplotype caller and several other parameters, now using the updated GATK. Hopefully, these will give me more compatible data sets, and I should be able to combine the .vcf information for each lane more effectively.

Haplotype Caller (Indx09)

/home/djacobse/jre1.7.0_67/bin/java -Xmx2g -jar /home/djacobse/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R /media/Ext12T/GenomeDB/HsGenome/resources/human_g1k_v37.fasta \
-I Indx09.fixed.bam \
--emitRefConfidence GVCF \
--variant_index_type LINEAR \
--variant_index_parameter 128000 \
-o Indx09.raw.snps.indels.g.vcf

This command worked well, so I'm going to run everything else as a bash script and finish up.

Bash script for running all indexes