GATK4 VariantRecalibrator resource error
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5.4 years ago

My following command

java -Xmx10g -Djava.io.tmpdir=Varcalling/cohort.vcf_VQSR -jar gatk-package-4.0.1.2-local.jar VariantRecalibrator -R /xxx/REFERENCES/hg19//bwa_index/hg19.fa -V Varcalling/cohort.vcf -resource hapmap,VCF,known=false,training=true,truth=true,prior=15.0 /xxx/REFERENCES/hg19/hapmap_3.3.hg19.sites.reorder.vcf -resource omni,known=false,training=true,truth=false,prior=12.0 /xxx/REFERENCES/hg19//1000G_omni2.5.hg19.sites.reorder.vcf -resource dbsnp,known=true,training=false,truth=false,prior=6.0 /xxx//REFERENCES/hg19//dbsnp_138.hg19.reorder.vcf -resource 1000G,known=false,training=true,truth=false,prior=10.0 /xxx//REFERENCES/hg19//1000G_phase1.snps.high_confidence.hg19.sites.reorder.vcf -an SOR -an QD -an MQRankSum -an ReadPosRankSum -an MQ  -an FS -an DP -mode SNP -O Varcalling/cohort.vcf.SNP.recal --tranches-file Varcalling/cohort.vcf.SNP.tranches --rscript-file Varcalling/cohort.vcf.SNP.plots.R

gives an error for the resource

 `***********************************************************************

A USER ERROR has occurred: Invalid argument '/sc/orga/projects/PBG/REFERENCES/hg19/hapmap_3.3.hg19.sites.reorder.vcf'.

***********************************************************************

I've tried changing it all the following but keep getting errors

 --resource hapmap,VCF,known=false,training=true,truth=true,prior=15.0 /xxx/REFERENCES/hg19/hapmap_3.3.hg19.sites.reorder.vcf

same error for above.

OR

 --resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 /xxx/REFERENCES/hg19/hapmap_3.3.hg19.sites.reorder.vcf

the error here is

A USER ERROR has occurred: The argument: "resource/resource" does not accept tags: "hapmap,VCF,known=false,training=true,truth=true,prior=15.0"

Anyone know what the mistake is that I am making here?

GATK4 NGS WES • 5.3k views
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Have a look at this thread

Basically you need a : between resource parameters and the resource path:

--resource hapmap,VCF,known=false,training=true,truth=true,prior=15.0:/xxx/REFERENCES/hg19/hapmap_3.3.hg19.sites.reorder.vcf

Although this also depends on your version of GATK...

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It worked for me with a a singly hyphen before resource and no 'VCF' in the tags, like so, -resource hapmap,known=false,training=true,truth=true,prior=15.0:$HapMap_Sites

I have a similar syntax question, if its acceptable to ask here as a follow-up. HaplotypeCaller is supposed to be able to take a VCF as a comp track, I've been unable to do so without error. Only my -dbSNP argument works. from the documentation -> e.g. -comp:FOO will have 'FOO' in the INFO field). Records that are filtered in the comp track will be ignored. Note that 'dbSNP' has been special-cased (see the --dbsnp argument).

$GATK HaplotypeCaller \
        -I $INP \
        -O $OUTPUT \
        -R $REF \
        -L $Targets \
        -ERC GVCF \
        --dbsnp $DBSNP138 \
       -comp:hapmap3.3 $HapMapV3VCF \
        $infofields

Here too I've tried various combinations of spaces and colons in between -comp and the variable. Any thoughts. Is this even an important resource to use during Haplotype calling?

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Don't do much germline mutation calling, but I think ExAC might have superseded HapMap? No idea WRT -comp. I highly recommend the GATK website, it's a bit of a mess because of versioning but the users and mods are very active, and because it's GATK your error will have occurred for others and almost certainly will have a Q/A on there.

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Thanks, I'll go through their forum again, I've looked through before and couldn't find my query there. I can't register to post a question on GATK website, since I don't have a uni/org email (am a contractor).

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Hello samreen.jasvi!

We believe that this post does not fit the main topic of this site.

Question solved.

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5
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3.7 years ago
DareDevil ★ 4.3k

In the latest version of GATK, there is a slight change in the syntax. You need to add : after resource and replace : with space in the begining of path to resource file.

Edit: the version is GATKv4.1

#!/bin/bash

reference="/path/to/Data/Homo_sapiens_assembly38.fasta"
interval='/path/to/Data/targetR.interval_list'
DBSNP='/path/to/Data/dbsnp_138.hg38.vcf.gz'
hapmap='/path/to/Data/hapmap_3.3.hg38.vcf.gz'
omni='/path/to/Data/1000G_omni2.5.hg38.vcf.gz'
thousand='/path/to/Data/1000G_phase1.snps.high_confidence.hg38.vcf.gz'


gatk --java-options '-Xmx24g' VariantRecalibrator -R $reference \
    -V input_raw.vcf.gz \
    --resource:hapmap,known=false,training=true,truth=true,prior=15.0 $hapmap \
    --resource:omni,known=false,training=true,truth=true,prior=12.0 $omni \
    --resource:1000G,known=false,training=true,truth=false,prior=10.0 $thousand \
    --resource:dbsnp,known=true,training=false,truth=false,prior=2.0 $DBSNP \
    -an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum \
    --mode SNP \
    -tranche 100.0 \
    -tranche 99.9 \
    -tranche 99.0 \
    -tranche 90.0 \
    -O recalibrate_SNP.recal \
    --tranches-file recalibrate_SNP.tranches \
    --rscript-file recalibrate_SNP_plots.R
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when you referring to latest, it would be nice to put the version name also

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Can you please explain the reasoning behind when you place =true or =false for the known, training and truth parameters?

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read this

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