Changes between Version 3 and Version 4 of SOPs/variant_calling_GATK

Timestamp:

01/16/14 15:53:47 (11 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling_GATK

@@ -43 +43 @@
   * bsub samtools index Reads_1.bwa.dedup.good.bam
 \\
-'''Run Indel Realignment''' (with RealignerTargetCreator and IndelRealigner) \\
+'''Run Indel Realignment''' (with [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_RealignerTargetCreator.html|RealignerTargetCreator]] and [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_IndelRealigner|IndelRealigner]]) \\
   * Example 1: java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T RealignerTargetCreator -R human.fasta -I original.bam -known indels.vcf -o realigner.intervals \\
   * Example 2: java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T IndelRealigner -R human.fasta -I original.bam -known indels.vcf -targetIntervals realigner.intervals -o realigned.bam \\
@@ -49 +49 @@
   * java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T IndelRealigner -R /path/to/genome/genome.fa -I Reads_1.bwa.dedup.good.bam -targetIntervals Reads_1.realigner.intervals -o Reads_1.bwa.dedup.realigned.bam --fix_misencoded_quality_scores
 \\
-'''Run Base Recalibration''' (BaseRecalibrator and PrintReads) \\
+'''Run Base Recalibration''' ([[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_BaseRecalibrator.html|BaseRecalibrator]] and [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.html|PrintReads]]) \\
   * Example 1: java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R human.fasta -I realigned.bam -knownSites dbsnp137.vcf -knownSites gold.standard.indels.vcf -o recal.table
   * Example 2: java -jar GenomeAnalysisTK.jar -T PrintReads -R human.fasta -I realigned.bam -BQSR recal.table -o recal.bam \\
@@ -57 +57 @@
   * Example 4: java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R human.fasta -before recal.table -after after_recal.table -plots recal_plots.pdf
 \\
-'''Compress BAM with ReduceReads''' [Optional] \\
+'''Compress BAM with [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html|ReduceReads]]''' [Optional] \\
   * Example 1: java -jar GenomeAnalysisTK.jar -T ReduceReads -R human.fasta -I recal.bam -o reduced.bam
   * java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T ReduceReads -R /path/to/genome/genome.fa -I Reads_1.bwa.dedup.realigned.recal.bam -o Reads_1.bwa.dedup.realigned.recal.reduced.bam
 \\
 '''Finally -- Call variants''' \\
-Run HaplotypeCaller ("The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper.")
+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.")
   * 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/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
 
-[If needed] Run UnifiedGenotyper should be a better choice for nondiploid samples and high sample numbers
+[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
   * 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/gatk/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
 \\
-'''Run Variant Quality Score Recalibration''' ("VQSR", with VariantRecalibrator and ApplyRecalibration) \\ \\
+'''Run Variant Quality Score Recalibration''' ("VQSR", with [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_VariantRecalibrator.html|VariantRecalibrator] and [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_ApplyRecalibration.html|ApplyRecalibration]) \\ \\
 '''Run Genotype Phasing and Refinement''' \\ \\
-'''Run Functional Annotation''' (snpEff and VariantAnnotator [which "parses output from snpEff into a simpler format that is more useful for analysis"])
+'''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"])
   * 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
 
-'''Analyze variant calls''' (with CombineVariants, SelectVariants, and VariantEval) \\ \\
+'''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]]) \\ \\