Changes between Version 49 and Version 50 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
09/05/17 14:03:21 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v49 v50  
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     91 {{{java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T PrintReads  -R /path/to/genome/fasta -I dedupped.bam -BQSR recalibration.table -o recalibrated.bam}}}
     92
     93
     94'''3 - Call and Filter Variants'''
     95
     96{{{java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T HaplotypeCaller  -R /path/to/genome/fasta -I  recalibrated.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -o Variants_called.vcf}}}
     97
     98{{{java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T VariantFiltration -R /path/to/genome/fasta -V  Variants_called.vcf -window 35 -cluster 3 -filterName Filter -filter "QD < 2.0" -filterName Filter -filter "FS > 30.0" -o Filtered_variants_called.vcf}}}
     99