Changes between Version 11 and Version 12 of SOPs/variant_calling_GATK


Ignore:
Timestamp:
07/13/15 11:28:06 (10 years ago)
Author:
gbell
Comment:

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  • SOPs/variant_calling_GATK

    v11 v12  
    7878  * java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T HaplotypeCaller -R /nfs/genomes/a.thaliana_TAIR_10/fasta_whole_genome/TAIR10.fa -I Reads_1.bwa.dedup.realigned.recal.reduced.bam --dbsnp SNPs_from_NCBI.sorted.vcf -o Reads_1.bwa.raw.snps.indels.HaplotypeCaller.vcf -stand_call_conf 30 -stand_emit_conf 10 -minPruning 3
    7979
     80Pay attention to the INFO lines printed when the command is complete to be sure that to many reads aren't being unexpectedly filtered out.  Using reads mapped by STAR, for example, can result in almost all reads failing the HCMappingQualityFilter or the MappingQualityUnavailableFilter.  A quick fix is to set the mapping quality of all reads to some value (like 60) on the fly by adding the arguments "-rf ReassignMappingQuality -DMQ 60".
     81
    8082[If needed] Run [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html|UnifiedGenotyper]] should be a better choice for nondiploid samples and high sample numbers
    8183  * Example: java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R human.fasta -I input.bam -o output.vcf -stand_call_conf 30 -stand_emit_conf 10