Question: haplotypecaller can not run in single bam file
0
gravatar for deepaksrna
29 days ago by
deepaksrna20
Argentina
deepaksrna20 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 • 131 views
ADD COMMENTlink modified 28 days ago • written 29 days ago by deepaksrna20

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

ADD REPLYlink modified 28 days ago • written 28 days ago by deepaksrna20

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

ADD REPLYlink written 28 days ago by genomax51k

How did you obtain the bam?

ADD REPLYlink written 28 days ago by WouterDeCoster30k

Print reads output bam

ADD REPLYlink written 28 days ago by deepaksrna20

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

ADD REPLYlink written 28 days ago by genomax51k
1
gravatar for egeulgen
28 days ago by
egeulgen410
Istanbul
egeulgen410 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 28 days ago by egeulgen410
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