Comments (3)
GenomicsDBImport is definitely the way to go for this kind of operation. On the other hand STRs are quite prone to errors especially when higher ploidies are involved. You may wish to reduce them or even completely drop them if they are not of your interest.
from gatk.
hi @gokalpcelik
I used GenomicsDBImport to replace CombinedGVCFs, but it has new problems, GenotypeGVCFs for GenomicsDB is so slow, can only get 900K interval vcf in 9 hours. how can i speed it up.
waiting for your reply. hava a good day!
from gatk.
Hi again.
You should be able to split your variants into multiple intervals and import all intervals in parallel under different genomicsDB import instances. Those instances can then be genotyped in parallel and finally combined into a single callset. By this way you can get your variants faster. This method is called scatter-gather which is what we do and suggest.
I hope this helps.
Regards.
from gatk.
Related Issues (20)
- ApplyVQSR Exception thrown at a/some variation site(s) after INDEL VQSR
- PrintReads introduces N bases when encoding some CRAMs and changes sequence HOT 15
- PostprocessGermlineCNVCalls error HOT 2
- GenotypeGVCFs report java.lang.OutOfMemoryError: Java heap space while call incremental imported GenomicsDB HOT 3
- Prevent users enabling annotations with mismatching data type (flow etc) HOT 7
- VariantAnnotator IndexOutOfBoundsException
- [bug report] CNNScoreVariants can't continue HOT 1
- VCF row validation error on gCNV results HOT 9
- PackagesNotFoundError: The following packages are not available from current channels: HOT 3
- Funcotator - WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr....
- several genes are reported in "PREDICTED_LOF" for a balanced translocation HOT 3
- Docker container should allow use by non-privileged user HOT 2
- Funcotator gnomAD incoherent number of output fields
- CombineGVCFs meet error HOT 2
- Empty BAM after running SplitNCigarReads HOT 4
- Troubleshooting VCF Output Truncation Issue during GATK CombineGVCFs Process HOT 1
- GATK Tutorial#11682 reproduce different results HOT 2
- SoftClippedReadFilter Shows Filtering Result Opposite to Description. HOT 1
- BwaSpark parameter optimization HOT 1
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from gatk.