call haplotypes in GATK HaplotypeCaller

Question

[Peter Chung]

I am new in bioinformatics. I would like to call haplotypes in GATK HaplotypeCaller, however the output result is 0kb. Can anyone give me some advice how to do the haplotypes ? I am doing the WGS.

REF="refs/ucsc.hg19.fasta"
name="samples/sample-1"
gatk --java-options "-Xmx16g" HaplotypeCaller \
-R $REF \
-I ${name}.addRG.mkdup.recal.bam \
-ERC GVCF \
-O ${name}.g.vcf.gz \
-bamout ${name}.haplotypes.bam \
--bam-writer-type CALLED_HAPLOTYPES \
--do-not-run-physical-phasing false

I am wondering the haplotypes output file. should it be a vcf file or a bam file ? Thanks.

[finswimmer]

Hello,

which version of GATK are you running? Are there any warning/error messaging?

fin swimmer

[Peter Chung]

Hi finswimmer,

I am using GATK4, there are not any messages but the output is 0kb. Thanks.

[ATpoint]

GATK (like most stuff from Broad), is probably the most talky (verbosity) tool I ever came across. There must be something unless you redirected stderr somehow.