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- Charles Chung
Hi Sheila, Thank you for your answer. The original HapMap files use 'chr1' not '1' for chromosome annotation, although it says it used b36. This causes GATK to complain and produce this error message: ERROR ----------------------------------------…
Hi, I was wondering what the differences are between IndelRealigner vs. LeftAlignAndTrimVariants. Is running one of the two sufficient for accurate indel calling? I have my own understanding of the two modules but want to be clarified by GATK team …
well, I was remembering the old ways to do it forgetting now that we have LiftoverVariants module.. It was successfully done using LiftoverVariants, so please disregard this posting..Thanks
without specifying a tmp folder still gives the same error...
liftOverVCF.pl and sortByRef.pl is under the same directory as gatk directory I used.
GATK version is (version 2.2-8-gec077cd) and the command line as follows: perl liftOverVCF.pl -vcf my.vcf \ -chain Liftover_Chain_Files/b37tohg19.chain \ -out mynew.vcf \ -gatk /usr/local/GATK \ -newRef hg19_canonical \ -oldRef human_g1k_…
Hi I was wondering what went wrong with my command to lift a VCF file: The script stops with a message: Re-sorting the vcf... Unknown option: tmp The sorting step failed. Please correct the necessary errors before retrying. So I did sorting using…