Changes between Version 10 and Version 11 of SOPs/variant_calling_GATK

Timestamp:

06/22/15 11:06:41 (10 years ago)

Author:

thiruvil

Comment:

--

SOPs/variant_calling_GATK

@@ -69 +69 @@
 
 \\
-11 - '''Compress BAM with [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html|ReduceReads]]''' [Optional] \\
+11 - '''Compress BAM with [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html|ReduceReads]]''' [Optional: this step is not available in GATK Version 3.0 and higher] \\
   * 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
 \\
 12 - '''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.")
+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)
   * 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