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  • Hi @Sheila , Thanks for replying. However, in my case, it did not automatically perform phasing. I used this command to run on my RNA Seq data: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R $genomeFasta -I $Input_BAM -dontUseSoftClippedBases …
  • Hello, If I am also interested in phasing of those SNPs that called from this pipeline, can I just enable --emitRefConfidence GVCF? Or I just use the exactly same pipeline, use ReadsBackedPhasing? Thanks!