HaplotypeCaller output mode

Question

[puddingmeow516]

Hi,

I used GATK HaplotypeCaller to call both variant and non-variant sites in a specific region with the code below:

gatk HaplotypeCaller --heterozygosity 0.004 -ERC BP_RESOLUTION --native-pair-hmm-threads 16 -L 12:20140000-23600000 -I $bamdir/${i}.bam -O $outdir/${i}.vcf -R $refseq

Then I tried the other two modes: EMIT_ALL_ACTIVE_SITES, EMIT_ALL_CONFIDENT_SITES based on the code above, separately. For both of tests, I got 237 more sites with and alternative allele in the ATL column compared to the output-mode EMIT_VARIANTS_ONLY.

My objective is to do the calling to ensure specific coordinates have NO SNPs, and identify the possibility of mapping failure. Bearing this objective, which output-mode is a better choice?

Thanks in advance!

Answer 1

[Pierre Lindenbaum]

you want --include-non-variant-sites https://gatk.broadinstitute.org/hc/en-us/articles/360040509751-GenotypeGVCFs#--include-non-variant-sites

[puddingmeow516]

Yes, thank you for your reply. I understand I have to use this parameter when I do joint genotyping using GenotypeGVCFs. I didn't make my words clear in the question, my current step is doing variant calling and getting GVCF for each sample, separately, and then I will combine and joint genotyping for a single VCF. I am quite confused that at my current step, except from adding BP_RESOLUTION, do I have to include output-mode as ACITVE/CONFIDENT?