- London, UK
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- London, UK
- Full Name
- Kirill Danilov
@bhanuGandham Thank you but it is neither a bug fix nor a workaround which I definitely cannot accept. I explicitly mentioned the fact that I use --include-non-variant-sites argument because I need it. And GenotypeGVCFs (GATK 22.214.171.124) works perfectl…
@bhanuGandham Any news?
@bhanuGandham Ok, surely the issue persists as it was not debugged during the old-gatk3-support-times. The output from HaplotypeCaller (GATK 126.96.36.199 with --emit-ref-confidence BP_RESOLUTION -genotyping-mode DISCOVERY --output-mode EMIT_ALL_CONFIDE…
Great change! It would be nice to have ALL GATK3 tools in GATK4 before the transition. Unfortunately, several great GATK3-specific tools are still either not implemented or only partially implemented in GATK4. Parallelism is also a great concern in …
Hi there. Same issue with one-sample human data genotyping using HaplotypeCaller from GATK 188.8.131.52 with --emit-ref-confidence BP_RESOLUTION. The resulting gVCFs are genotyped using GenotypeGVCFs from GATK 3.8 (yeah, it supports parallelization at l…
Hi @bhanuGandham I guess a figured this out. The speed of DepthOfCoverage analysis is severely and mostly limited by writing out the depth at each base argument, hence disabling --omitIntervalStatistics and enabling -nt basically do not improve th…
@bhanuGandham thank you for your reply. Since DepthOfCoverage has not been implemented in GATK4 yet, I’m using GATK3.8, obviously. So there’s no support for the tools that have not been deprecated though are necessary and have no analogs in the ne…
Dear @Geraldine_VdAuwera, I'm not quite sure if it is polite but I would be grateful if you could elaborate on this question when you have time.
Thanks, @shlee Actually, I'm already using GATK4 HaplotypeCaller for variant calling, it's explicitly mentioned in the code blocks above and in the text. I'm using only GenotypeGVCFs from GATK3.8 due to the above-mentioned reasons. I didn't quite …
The same error occurs when running the GATK 184.108.40.206 BaseRecalibrator with dbSNP VCF file processed (in any way) by bcftools. Bcftools adds contig ID fields to the VCF header without the corresponding lengths which causes the error. Deleting these li…