Question: haplotypecaller can not run in single bam file
2
gravatar for deepaksrna
14 months ago by
deepaksrna40
Argentina
deepaksrna40 wrote:

Hi all,

I an new to WGS analysis, i am trying to run haplotypecaller in one bam file.

java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R GRCh37/hs37d5.fa -I LG_GWG.1.bam  -D reference/gatkbundle/dbsnp_138.b37.vcf -o LG_GWG.output.g.vcf -ERC GVCF -nct 4

can anyone help me to figure out this issue. thanks

the error that put out :

ERROR MESSAGE: Invalid command line: Argument emitRefConfidence has a bad value: Can only be used in single sample mode currently. Use the sample_name argument to run on a single sample out of a multi-sample BAM file
gatk3 -erc wgs haplotypecaller • 1.1k views
ADD COMMENTlink modified 14 months ago • written 14 months ago by deepaksrna40

It works without GVCFspecification, but to generate the gvcf file I need the GVCF argument

ADD REPLYlink modified 14 months ago • written 14 months ago by deepaksrna40

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 14 months ago by genomax70k

How did you obtain the bam?

ADD REPLYlink written 14 months ago by WouterDeCoster40k

Print reads output bam

ADD REPLYlink written 14 months ago by deepaksrna40

What does that mean? Can you provide the actual commandline you used?

ADD REPLYlink written 14 months ago by genomax70k
1
gravatar for egeulgen
14 months ago by
egeulgen810
Istanbul
egeulgen810 wrote:

try omitting the -ERC GVCF argument or provide the sample name to sample_name argument if it's a multi-sample BAM file

ADD COMMENTlink written 14 months ago by egeulgen810
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