Changes between Version 22 and Version 23 of SOPs/variant_calling_GATK

Timestamp:

07/18/17 08:59:19 (8 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling_GATK

@@ -75 +75 @@
 \\
 11 - '''Finally -- Call variants''' \\
-Run [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_haplotypecaller_HaplotypeCaller.html|HaplotypeCaller]] ("The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper."; HaplotypeCaller is recommended as of GATK Version 3.0)
+Run [[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php|HaplotypeCaller]] ("The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper."; HaplotypeCaller is recommended as of GATK Version 3.0)
   * Example: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human.fasta -I input.bam -o output.vcf -stand_call_conf 30 -stand_emit_conf 10 -minPruning 3
   * java -jar /usr/local/gatk3/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 too many reads aren't being unexpectedly filtered out.  Using RNA-seq 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
+[If needed] Run [[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_genotyper_UnifiedGenotyper.php|UnifiedGenotyper]] may be a better choice for nondiploid samples and high sample numbers
   * Example: java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R human.fasta -I input.bam -o output.vcf -stand_call_conf 30 -stand_emit_conf 10 
   * java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T UnifiedGenotyper -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.UnifiedGenotyper.vcf -stand_call_conf 30 -stand_emit_conf 10
 \\
 12 - '''Run Variant Quality Score Recalibration''' ("VQSR", with 
-[[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php|VariantRecalibrator]] and [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_ApplyRecalibration.php|ApplyRecalibration]]) \\ \\
+[[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php|VariantRecalibrator]] and [[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantrecalibration_ApplyRecalibration.php|ApplyRecalibration]]) \\ \\
 13 - '''Run Genotype Phasing and Refinement''' \\ \\
-14 - '''Run Functional Annotation''' ([[http://snpeff.sourceforge.net/SnpEff.html|snpEff]] and [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html|VariantAnnotator]] [which "parses output from snpEff into a simpler format that is more useful for analysis"])
+14 - '''Run Functional Annotation''' ([[http://snpeff.sourceforge.net/SnpEff.html|snpEff]] and [[https://software.broadinstitute.org/gatk/gatkdocs/current/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php|VariantAnnotator]] [which "parses output from snpEff into a simpler format that is more useful for analysis"])
   * Example 1: java -jar snpEff.jar eff -v -onlyCoding true -i vcf -o gatk GRCh37.64 input.vcf > output.vcf
   * Example 2: java -jar GenomeAnalysisTK.jar -T VariantAnnotator -R human.fasta -A SnpEff --variant original.vcf --snpEffFile snpEff_output.vcf -o annotated.vcf
 
-15 - '''Analyze variant calls''' (with [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_CombineVariants|CombineVariants]], [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html|SelectVariants]], and [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_varianteval_VariantEval.html|VariantEval]]) \\ \\
+15 - '''Analyze variant calls''' (with [[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php|CombineVariants]], [[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php|SelectVariants]], and [[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_varianteval_VariantEval.php|VariantEval]]) \\ \\