Changes between Version 20 and Version 21 of SOPs/variant_calling_GATK

Timestamp:

07/14/17 11:54:51 (8 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling_GATK

@@ -93 +93 @@
   * 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
 \\
-13 - '''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]) \\ \\
+13 - '''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]]) \\ \\
 14 - '''Run Genotype Phasing and Refinement''' \\ \\
 15 - '''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"])