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Out of curiosity, I am looking at adding the Axiom resource to my indel VQSR (WGS on hg19). Is the hg38 bundle version, Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz (ftp), a curated resource? I was thinking about using the ExAC-hoste…
@Sheila Hi Sheila, thank you for the update. Sorry about pulling up an old thread. I'll look into using ExcessHet as a hard filter, a threshold of 54.69 would remove approx 1.5% of ~60m sites. Comments here and here seem to elaborate on the ExcessH…
(Quote) @Geraldine_VdAuwera does best practices reflect this update regarding InbeedingCoeff somewhere? I don't see it on broadinstitute.org or in the GATK presentations on Google Drive. Digging a little further, it looks like gatk-workflow/gatk4-g…
@JinboWuGlasgow In my case, I had to override my PATH (and possibly JAVA_HOME) to run GATK on a local JDK 8. env PATH=~/my_jdk8/bin:$PATH JAVA_HOME=~/my_jdk8 /path/to/gatk ... The java_home command in the article didn't help much, since my java_h…
(Quote) Step 2 mentions -I realigned_reads.bam. Is this also supposed to be the same BAM from Step 1 (input_reads.bam)? Or have I overlooked an input?
For those searching in 2017, the liftover chain files are not in the bundle, you can find them at ftp://ftp.broadinstitute.org/Liftover_Chain_Files