GATK HaplotypeCaller for non-model organism: gVCF output
Hi,
Thank you for the best practices documentation. For single-sample variant calling for a non-model organism, is it correct that one can use HaplotypeCaller to generate a gVCF and skip the GenotypeGVCFs step? Or do you still need to GenotypeGVCFs for this single sample?
I am also wondering if the argument `--output-mode EMIT_ALL_CONFIDENT_SITES` has an effect with the argument `ERC GVCF`?
Thank you very much for your help and all the best.
Katie
REQUIRED for all errors and issues:
a) GATK version used: 4.1
b) Exact command used:
gatk --java-options "-Xmx4g" HaplotypeCaller \
-R ${reference} \
-ploidy ${params.ploidy} \
-I ${bam} \
-ERC GVCF \
--output-mode EMIT_ALL_CONFIDENT_SITES \
-O ${sample_id}_gatk.g.vcf.gz
c) Entire program log: Program runs as expected, just clarifying argument meanings.
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