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- Sai Mukund
This is the docker container i used: quay.io/biocontainers/gatk4:220.127.116.11--0. So i am guessing its GATK 18.104.22.168. This is the exact command i ran: gatk GenomicsDBImport -R /gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa9…
When I'm running picard MergeBamAlignment, I am getting this error Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.util.zip.DataFormatException: invalid distance too far back. Any idea on what this could be and h…
Is there a way to run HaplotypeCaller for multiple reads in a bam file. When i run the HaplotypeCaller the output vcf provides the SNV hits but with no read ID. I am not able to figure out which SNV corresponds to which read of the bam file.