How to force GATK haplotypecaller to output all genomic position (even non variant positions)

Question

[Nicolas Rosewick]

Hi,

Is there a way to force GATK haplotypecaller to output all genomic positions in the vcf; not only variant ones ?

Example here :

Top : Raw bam file

Middle : -outbam using : gatk HaplotypeCaller -R $genome -O test.vcf -I in.bam -ERC GVCF --max-alternate-alleles 3 -bamout test.bam -L interval.bed --output-mode EMIT_ALL_ACTIVE_SITES

bottom : -outbam using gatk HaplotypeCaller -R $genome -O test.vcf -I in.bam -ERC GVCF --max-alternate-alleles 3 -bamout test.bam -L interval.bed --output-mode EMIT_ALL_CONFIDENT_SITES

You can see that the region without variant sites are not processed by haplotypecaller ; even with EMIT_ALL_ACTIVE_SITES and EMIT_ALL_CONFIDENT SITES.

Any idea how to tune haplotypecaller to output all sites with enough coverage ?

gatk version : 4.1.7.0

Thanks

Answer 1

[curious]

gatk HaplotypeCaller -R {reference} -I {bam_path} -L {bed_path} -ERC BP_RESOLUTION -O {out_vcf}

Maybe look at BP_RESOLUTION