You can follow my NGS tools from docker hub keyword skysbiodocker.
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When you use a bed file for these tools to jump from region to region HTSJDK requires a proper index to handle the lookup tables from the vcf index. A proper vcf index for jumping regions also requir… (View Post)
Some parts of the gatk package comes from picard which uses a seperate command line argument consensus still compared to original gatk tools. You may need to bear with it for a while until complete m… (View Post)
Not all vcf parsers do a good job in keeping the format intact that's why. When I joint analyze my CNV vcf files I convert them to tabular format (using my custom tool using HTSJDK so format is alway… (View Post)