amitgsir

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amitgsir
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Busan, South Korea
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  • Yeah, I missed the trick. It's working fine now. thanks @shlee~~
  • Sorry, file was not uploaded due to filetype issue. Edited the above comment.
  • Hi, Attached is the my wdl script. I am running BaseRecalibrator (and post baserecal), PrintReads and Mutect2 by scattering the BAM file using the genomic region bed file for each chomosome. After PrintReads I can find the bam and bai (index) file …
  • Hi, is there any way to scatter by contig or region (-L Interval List). I want to use scatter in Variant Calling by specifying the interval_region (by -L), but can not foing how to use in wdl. Amit
  • Hi, I am still getting error. This is how my script looks like: import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.extensions.gatk._ import org.broadinstitute.variant.variantcontext.VariantContext.Type import org.bro…
  • I think, I am having trouble with "import the correct type object". Is there any documentation regarding how or what to import for each tools/GATK Walker. I couldn't find any working information. For most of the solution provided, the im…
  • Hi, I am trying to use Queue for Variant Calling and then Hard-Filtering. So, I am trying to select the variants by INDEL and SNPs in two steps. Below is my scala script: import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.…