Question: call haplotypes in GATK HaplotypeCaller
0
gravatar for Peter Chung
13 months ago by
Peter Chung90
Hong Kong
Peter Chung90 wrote:

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.

ADD COMMENTlink written 13 months ago by Peter Chung90

Hello,

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

fin swimmer

ADD REPLYlink written 13 months ago by finswimmer13k

Hi finswimmer,

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

ADD REPLYlink written 13 months ago by Peter Chung90

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.

ADD REPLYlink written 13 months ago by ATpoint34k
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: 1836 users visited in the last hour