haplotypecaller can not run in single bam file

Question

[deepaksrna]

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

[deepaksrna]

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

[GenoMax]

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

[WouterDeCoster]

How did you obtain the bam?

[deepaksrna]

Print reads output bam

[GenoMax]

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

Answer 1

[egeulgen]

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