Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

Regards
GATK Staff

minxiong

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minxiong
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Comments

  • 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!