haplotypecaller can not run in single bam file
1
2
Entering edit mode
3.4 years ago
deepaksrna ▴ 40

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
haplotypecaller gatk3 -ERC WGS • 3.3k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

How did you obtain the bam?

ADD REPLY
0
Entering edit mode

Print reads output bam

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
3.4 years ago
egeulgen ★ 1.1k

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

ADD COMMENT

Login before adding your answer.

Traffic: 1635 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6