Comments (5)
I am considering sharing the lanelet crams for samples: AV0148-C and AV0079-C. Their indel realigned bams both have average coverage of ~2.5x, and thus both failed sampled QC. Both have very few called genotypes. We can definitely use these samples to test plumbing of IRODS import --> alignment --> UnifiedGenotyper.
Do you suspect the lack of genotype calls will cause these samples to crash the new phasing pipeline?
For testing just plumbing of alignment -->UnifiedGenotyper, we can downsample those crams to just a single chromosome.
from pipelines.
Thanks Thuy.
(below applies to shapeit2
only. I am unsure of the behaviour of shapeit4
)
Shapeit2
reports an error when all of the genotypes in a dimension are missing. ie a sample with all missing genotypes, or a genotype missing in all samples.
Phasing just 2 samples both with high missingness, would almost certainly meet this condition. That being said, it's very possible that a GT call may be missing in all samples in the whole set, so may well need consideration regardless and not just in this minimal case.
We hit this mainly when we were running single samples against a reference panel. In that case, any missing genotypes were problematic.
from pipelines.
I've decided to leave the samples AV0148-C and AV0079-C as is without downsampling, since they are 3 orders of magnitude smaller than the existing samples we've provided: AN0131-C and AB0252-C. Per-lanelet bams of ~1.7GB vs 2.5MB.
from pipelines.
from pipelines.
Now that we've started doing batch processing of multiple samples at once, we need more plumbing samples. We have about 2 really small samples. We need at least 4.
@magnusmanske We can use AV0148-C and AV0079-C for quick batch processing testing. That allows to have 1 sample per batch. I'll try to find 2 samples so that we can have at least 2 samples per batch.
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Related Issues (20)
- Number of SNPs and Indels doesn't match with the numbers reported in README files HOT 4
- Provide example crams released by Core Sequencing HOT 3
- Define read group contents in vector short read alignment pipelines HOT 1
- Input source for mosquito short read alignment pipeline HOT 3
- Validation/truth datasets for variant calling calibration, comparison and evaluation HOT 26
- Copy script to convert vcf to zarr to this repo
- Port baseline Plasmodium amplicon SNP calling pipeline. HOT 1
- Add platform argument to build_pipeline_release script HOT 2
- How to make bwa short read alignment deterministic for testing HOT 1
- Mosquito phasing pipeline development HOT 22
- Genotype Concordance Validation of genotyping pipelines HOT 10
- Create pipelines that download multiple samples from IRODS in a batch
- Determine final lanelet manifest fields required for vector alignment and genotyping HOT 1
- Cromwell configurations on farm5 are using localization = copy, which explodes size of workflow working directory
- Convert cram to bam in vector alignment pipeline
- malaria-dk lsf group deprecated
- Output of vector short read alignment pipeline is named *.bam.bam HOT 1
- Use flexible fields in manifest
- Validate results for phasing pipeline HOT 17
- Ag3.0 phasing pipeline production run HOT 15
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