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minxiong

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minxiong
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  • Thanks!
  • java -jar /data/software/gatk-3.3/GenomeAnalysisTK.jar -T HaplotypeCaller -R ucsc.hg19.fasta -I sample1_PrintReads.bam -stand_emit_conf 10 -stand_call_conf 30 -o raw_sample1.vcf
  • I didn't find 0/0 in VCF file. I don't know why?
  • Yes, I followed GATK Best Practices. I used bwa mem, SortSam, MarkDuplicates, AddOrReplaceReadGroups, AddOrReplaceReadGroups, RealignerTargetCreator, IndelRealigner, BaseRecalibrator, PrintReads, HaplotypeCaller for 48 samples. After HaplotypeCall…
  • Hi Sheila, This is my workflow: java -jar /data/software/picard/SortSam.jar INPUT=sample.sam OUTPUT=sample1.bam SORT_ORDER=coordinate java -jar /data/software/picard/MarkDuplicates.jar INPUT=sample1.bam OUTPUT=sample1_dedup.bam METRICS_FILE=met…
  • Hi Sheila, Thanks for reply. maybe GATK 3.3. How to check? Thanks, Min
  • Hi tommycarstensen, Thanks for your reply. But I still fell command is not right. java -jar /data/software/picard/MarkDuplicates.jar INPUT=sample1.s am OUTPUT=sample1_dedup.bam SO=coordinate But I got it from paper "From FastQ data to high confi…
  • Thanks for your reply!