hg38 alt aware mode
Hello,
I'm trying to follow the instruction at:
https://gatk.broadinstitute.org/hc/en-us/articles/360037498992?id=8017
and having an error as follows:
Can you please provide
a) GATK version used
3.5
b) Exact GATK commands used
java -Xms4g -Xmx4g -jar /software/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T HaplotypeCaller -R reference/Homo_sapiens_assembly38.fasta -o sample/R3032/g.vcf -I sample/R3032/snaut.bam -ERC GVCF --max_alternate_alleles 3 --read_filter OverclippedRead --emitDroppedReads -bamout sample/R3032/hc.bam
c) The entire error log if applicable.
##### ERROR MESSAGE: Argument with name 'emitDroppedReads' isn't defined.
Shouldn't I provide the option, "--emitDroppedReads"?
Also will you provide the instruction with GATK version 4 soon?
Thank you!
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Hi hirokomatsui
Please upgrade to the latest version GATK4. We do not support GATK 3 anymore.
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Yes, I have version 4 too.
I don't know how to adjust some commands from version 3 to 4 in the instruction:
https://gatk.broadinstitute.org/hc/en-us/articles/360037498992?id=8017Any plan to update the page for version 4?
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Hi hirokomatsui
Yes we are looking into updating this doc. Thank you for pointing that out.
In the meantime you can refer to the tooldocs for commands for the latest version: https://gatk.broadinstitute.org/hc/en-us/articles/360040507431--Tool-Documentation-Index
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Thank you, I'm looking for the update!
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