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How to create a Haplotype file from HaplotypeCaller

peterchungpeterchung Member
edited April 2019 in Ask the GATK team
I am new to use GATK4. I would like to generate a Haplotype file (.bam or vcf file with haplotype information). I followed the Best Practice step till haplotypecaller.

REF="refs/ucsc.hg19.fasta"
name="sample1"

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

However, the bamout output file is 0kb and there is not warning/error messages.
Is it a create a ${name}.haplotypes.bam bam file with haplotype information ?
or how can i generate a vcf file with haplotype information ("0|1" or with PS")?

Thanks.

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