Gatktools

Question

[bestone]

Hello guys, I run this code to get vcf file

gatk HaplotypeCaller -R reference_genome.fasta -I input.bam -O variants.vcf

But unfortunatelly it has given error code like this;

A USER ERROR has occurred: Fasta dict file file:///Users/uguremre/gatk-4.4.0.0/reference_genome.dict for reference file:///Users/uguremre/gatk-4.4.0.0/reference_genome.fasta does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.

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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace

What can I do to solve this issue? Thank you

[Pierre Lindenbaum]

It says:

reference_genome.dict for reference /reference_genome.fasta does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it

ok. I must admit that the page has moved. But the page is now available here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531652-FASTA-Reference-genome-format

also, duplicate of GATK HaplotypeCaller Error

[bestone]

my gatk is working and I run this code but it is telling gatk-lunch not found gatk-launch HaplotypeCaller \ -R reference_genemo.fasta \ -I input.bam \ -O output.vcf

[Pierre Lindenbaum]

what is gatk-launch ?

[bestone]

I want to get vcf file I found this code to make vcf file. Could you pls help me to get vcf file. I couldn't figure it out