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Is your feature request related to a problem? Please describe.
In snappy-pipeline, a common problem with meta data is that assignment to families is (partially) incorrect. E.g., a trio might actually be processed as two disjoin families or samples may be swapped between families.
Describe the solution you'd like
A common resolution is to clear all work and output file that contain the samples in the families. Tools support would be nice.
With knowledge about the snappy-pipeline structure, look for all work and output files that have sample names in them (e.g., .ped or .vcf.gz files).
Collect a list of such files and ask user to confirm to delete them (add a --yes parameter to answer question(s) with yes).
Remove files if user confirmed.
Describe alternatives you've considered
N/A
Additional context
In some cases, it may be necessary to remove "merge" in steps as well.
The text was updated successfully, but these errors were encountered:
Is your feature request related to a problem? Please describe.
In snappy-pipeline, a common problem with meta data is that assignment to families is (partially) incorrect. E.g., a trio might actually be processed as two disjoin families or samples may be swapped between families.
Describe the solution you'd like
A common resolution is to clear all
work
andoutput
file that contain the samples in the families. Tools support would be nice.work
andoutput
files that have sample names in them (e.g.,.ped
or.vcf.gz
files).--yes
parameter to answer question(s) withyes
).Describe alternatives you've considered
N/A
Additional context
In some cases, it may be necessary to remove "merge" in steps as well.
The text was updated successfully, but these errors were encountered: