Changes between Version 13 and Version 14 of SOPs/variant_calling_GATK

Timestamp:

07/13/15 11:43:58 (10 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling_GATK

@@ -78 +78 @@
   * 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
 
-Pay attention to the INFO lines printed when the command is complete to check 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".
+Pay attention to the INFO lines printed when the command is complete to check that too 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 modify the mapping quality of reads with some value (like 255) to some other value (like 60) on the fly by adding the arguments "-rf ReassignOneMappingQuality -RMQF 255 -RMQT 60".  See the [[https://www.broadinstitute.org/gatk/blog?id=4285|GATK blog]] for more information.
 
 [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