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Make it easier to run downstream GATK calling on downsampled bams

Status: Open.

#14 In eriqande/mega-non-model-wgs-snakeflow;

· eriqande opened on Oct 23, 2024

Overhaul the downsampling to deal with duplicates

Status: Open.

#13 In eriqande/mega-non-model-wgs-snakeflow;

· eriqande opened on Oct 23, 2024

Downsampling step that makes hard links for bams that are already lower coverage than the target triggers re-runs when overlap clipped bai's have a later modification date than the bams

Status: Open.

#12 In eriqande/mega-non-model-wgs-snakeflow;

· eriqande opened on May 31, 2024

Experiment with archiving the BAMs as CRAMs

Status: Open.

#9 In eriqande/mega-non-model-wgs-snakeflow;

· eriqande opened on Feb 9, 2023

Allow for additional indels VCF

Status: Open.

#7 In eriqande/mega-non-model-wgs-snakeflow;

· eriqande opened on Oct 28, 2022