Changes between Version 57 and Version 58 of SOP/CallingVariantsRNAseq
- Timestamp:
- 09/06/17 07:42:01 (8 years ago)
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SOP/CallingVariantsRNAseq
v57 v58 70 70 {{{java -jar /usr/local/share/picard-tools/picard.jar AddOrReplaceReadGroups I=output.sam O=rg_added_sorted.bam SO=coordinate RGID=ID_NAME RGLB=library RGPL=illumina RGPU=identifier RGSM=sample_name}}} 71 71 72 '''Mark duplicate reads '''.72 '''Mark duplicate reads.''' 73 73 74 74 … … 76 76 77 77 78 '''Identify and split Cigar N Reads and reassign quality scores '''.78 '''Identify and split Cigar N Reads and reassign quality scores.''' 79 79 80 80 {{{java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T SplitNCigarReads -R /path/to/genome/fasta -I dedupped.bam -o split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS -fixMisencodedQuals}}} 81 81 82 82 83 '''Perform BaseRecalibration '''.\\83 '''Perform BaseRecalibration.''' \\ 84 84 Calibration files can be found here for hg38 [https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0 Recalibration Files]\\ 85 85 NOTE: Calibration Files are only available for a few genomes (Human, Mouse, etc). \\ … … 92 92 93 93 94 '''3 - Call and Filter Variants '''94 '''3 - Call and Filter Variants.''' 95 95 96 96 {{{java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T HaplotypeCaller -R /path/to/genome/fasta -I recalibrated.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -o Variants_called.vcf}}} … … 99 99 100 100 101 '''4 - Predict the effects of called variants ''' \\101 '''4 - Predict the effects of called variants.''' \\ 102 102 Several tools are available to analyze variants found in your .vcf result files for potential functional consequence. See details [http://barcwiki.wi.mit.edu/wiki/SOPs/vcf here].
