Comments (3)
silastittes
commented on May 28, 2024
1
I did not! You might give this new pipeline a try. The recalibration step appears to be optional.
https://arxiv.org/abs/2103.15167
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knokknok
commented on May 28, 2024
Hi, same use case here...
Did you manage to find a workaround?
Thanks!
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lczech
commented on May 28, 2024
Thanks @silastittes for mentioning my pipeline here! Indeed, it does not require known variants, and also offers a lot of other tools and settings. Maybe it helps @knokknok as well ;-)
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Related Issues (20)
- Erro in rule snpeff HOT 1
- README report link served through RawGit will stop working
- snpeff with custom genome database
- Direct output to directory of interest HOT 1
- Which singularity image is used? HOT 1
- Failed to open environment file
- Failed to open environment file mergevcfs HOT 1
- Haplotype caller with intervals runs slow HOT 2
- Not executed fastqc for specified inputs HOT 1
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- missing python dependency in rule plot_stats HOT 2
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- Error tokenizing data. C error: Expected 5 fields in line 4, saw 6 HOT 2
- TypeError in calling.smk rule merge_variants. The bwa mapping stops after creating the indexes files. HOT 7
- Help with dna-seq-gatk-variant-calling
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