Comments (3)
marcelm
commented on August 26, 2024
chr1 also doesn’t follow the pattern. Or is this an artifact?
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pontushojer
commented on August 26, 2024
Yeah its true chr1 also takes longer than expected. It was however not as striking as chrY but still this might relate to a shared issue.
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pontushojer
commented on August 26, 2024
I did a check for a separate dataset and compared against all other rules that are run for the chunks. Looking at this we see that chr1, chr16, chr21 (somewhat less though) and chrY stick out from the rest (see the red trace for clusterrmdup).
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Related Issues (20)
- Run for specific region only
- Add all parameters to configs? HOT 1
- Add phasing with HapTree-X
- Enble lariat as mapper for 10x and stLFR reads.
- Filter out barcodes not matching pattern. HOT 1
- Rule map_sort sometimes fails for ema
- where is chr1mini.fasta? HOT 1
- How to use wfa2tenx or BLR_metagenomics? HOT 2
- New phasing algorithm: SpecHap
- Update use of read groups
- Enable subsampling of input FASTQ HOT 1
- Make barcode merging configurable HOT 3
- starcode runs out of memory for large datasets HOT 4
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- Snakemake version >=6.5 does not schedule jobs optimally HOT 1
- Generate SV VCF as part of final output.
- Include software versions in report
- MultiQC 1.12 not compatible with BLR HOT 1
- gatk HaplotypeCaller filters out QUAL < 30 by default HOT 1
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