Question: haplotypecaller can not run in single bam file
0
gravatar for deepaksrna
5 months 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 • 436 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by deepaksrna20

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

ADD REPLYlink modified 5 months ago • written 5 months ago by deepaksrna20

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

ADD REPLYlink written 5 months ago by genomax59k

How did you obtain the bam?

ADD REPLYlink written 5 months ago by WouterDeCoster35k

Print reads output bam

ADD REPLYlink written 5 months ago by deepaksrna20

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

ADD REPLYlink written 5 months ago by genomax59k
1
gravatar for egeulgen
5 months ago by
egeulgen510
Istanbul
egeulgen510 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 5 months ago by egeulgen510
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1168 users visited in the last hour