Daniel:Notebook/Haplotyping/2014-8-22: Difference between revisions

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>Djacobse
(Created page with "=Microfluidics Data= Back to Calendar After much playing around with the errors, I've decided to scrap the variant recalibration. I noticed ...")
 
>Djacobse
Line 7: Line 7:
'''Haplotype Caller (Indx09)'''
'''Haplotype Caller (Indx09)'''


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

Revision as of 18:05, 22 August 2014

Microfluidics Data

Back to Calendar

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