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Revision as of 10:59, 29 October 2014
, 10:59, 29 October 2014→Results
* glfs with a bams & samples subdirectory
* glfs with a bams & samples subdirectory
* pvcfs with a subdirectory per chromosome and then per region
* pvcfs with a subdirectory per chromosome and then per region
* split with a subdirectory per chromosome
* '''split''' with a subdirectory per chromosome
* vcfs with a subdirectory per chromosome
* '''vcfs''' with a subdirectory per chromosome
* (optionally your target directory)
* (optionally your target directory)
Under the vcf/chrXX directory, there should be:
Under the '''vcf/chrXX''' directory, there should be:
* chrXX.filtered.sites.vcf
* chrXX.filtered.sites.vcf
* chrXX.filtered.sites.vcf.norm.log
* chrXX.filtered.sites.vcf.norm.log
* chrXX.filtered.sites.vcf.summary
* chrXX.filtered.sites.vcf.summary
* chrXX.filtered.vcf.gz
* '''chrXX.filtered.vcf.gz''' - final filtered variant call file
* chrXX.filtered.vcf.gz.OK
* chrXX.filtered.vcf.gz.OK
* chrXX.filtered.vcf.gz.tbi
* chrXX.filtered.vcf.gz.tbi
The filtered is the merged.vcf after it has been run through filters and is marked with PASS/FAIL.
The filtered is the merged.vcf after it has been run through filters and is marked with PASS/FAIL.
Under the split/chrXX directory, there should be:
Under the '''split/chrXX''' directory, there should be:
* chrXX.filtered.PASS.split.[N].vcf.gz
* chrXX.filtered.PASS.split.[N].vcf.gz
* chrXX.filtered.PASS.split.err
* chrXX.filtered.PASS.split.err
* chrXX.filtered.PASS.split.vcflist
* chrXX.filtered.PASS.split.vcflist
* chrXX.filtered.PASS.gz
* '''chrXX.filtered.PASS.gz''' - final variant call file with only PASS variants
* subset.OK
* subset.OK
