Changes between Version 51 and Version 52 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
09/05/17 14:12:28 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v51 v52  
    9494'''3 - Call and Filter Variants'''
    9595
    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}}}
     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}}}
    9797
    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}}}
     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}}}
    9999
    100100