Changes

This gives you the following files:

This gives you the following files:

* '''chr20.filtered.vcf.gz ''' - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL including per sample information

* '''chr20.filtered.vcf.gz ''' - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL including per sample genotypes

* chr20.filtered.sites.vcf - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL without the per sample information

* chr20.filtered.sites.vcf - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL without the per sample genotypes

* chr20.filtered.sites.vcf.log - log file

* chr20.filtered.sites.vcf.log - log file

* chr20.filtered.sites.vcf.summary - summary of filters applied

* chr20.filtered.sites.vcf.summary - summary of filters applied

Also in the $GCOUT/vcfs/chr20 directory are intermediate files:

Also in the $GCOUT/vcfs/chr20 directory are intermediate files:

* the whole chromosome variant calls prior to any filtering:  

* the whole chromosome variant calls prior to any filtering:  

** chr20.merged.sites.vcf - no sample information

** chr20.merged.sites.vcf - without per sample genotypes

** chr20.merged.stats.vcf  

** chr20.merged.stats.vcf  

** chr20.merged.vcf - includes sample information

** chr20.merged.vcf - including per sample genotypes

** chr20.merged.vcf.OK - indicator that the step completed successfully

** chr20.merged.vcf.OK - indicator that the step completed successfully

* 40000001.45000000 subdirectory contains the data for just that region.

* 40000001.45000000 subdirectory contains the data for just that region.