WebThe following examples show how to use htsjdk.samtools.SAMSequenceDictionary.You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. WebOct 23, 2024 · When I use touch for both of them I get this error: AmbiguousRuleException: Rules bwa_index and gatk_refdict are ambiguous for the file ref. Expected input files: bwa_index: ref.fasta gatk_refdict: ref.fasta. This is the code: rule bwa_index: input: database="ref.fasta" output: done =touch ("ref") shell: """ bwa index -p ref …
How can I prepare a FASTA file to use as reference?
Websuper(String.format("Fasta bgzip index file %s for reference %s does not exist. A gzi index can be created using bgzip.", gziPath.toUri(), fastaPath.toUri()));}} public static class MissingReferenceDictFile extends UserException {private … WebJan 13, 2024 · java -jar picard.jar CreateSequenceDictionary R=Homo_sapiens_assembly18.fasta O=Homo_sapiens_assembly18.dict. Run GATK … frozen 40
GATK HaplotypeCaller index 踩坑 - 简书
WebOct 1, 2015 · I need all the sequences present. Instead of cutting off at the 30th line, can you post all the sequences present in both the .dict file and vcf file. You can attach them as text files so they will not clutter the body of the question. Thanks, Sheila. P.S. I just need to make sure all the contigs present in your .dict file are present in your ... WebFeb 21, 2024 · They're not 3 different formats. .fai is the index of the .fa. .dict is a different format, sure. Run this command and then try your GATK command: cd ~/path/ ln -s ref.dict PitayaGenomic.dict. ADD REPLY • link 18 days ago by Ram 38k. 0. still same issue. java.lang.IllegalArgumentException: File is not a supported reference file type. ADD ... WebZip vcf file and create an index¶ A vcf file for the GATK pipeline needs to be sorted and contain the reference dictionary. It also should be zipped and provided an index file. These step are only required if your reference vcf file has not been prepared (the vcf files from the GATK bundle are already prepared for the pipeline). frozen 4 video