3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→STEP 3 : Run GotCloud Variant Calling Pipeline
** chr20.merged.vcf.OK - indicator that the step completed successfully
** chr20.merged.vcf.OK - indicator that the step completed successfully
* the hardfiltered (pre-svm filtered) variant calls:
* the hardfiltered (pre-svm filtered) variant calls:
** chr20.filtered.vcf.gz - vcf for whole chromosome after it has been run through hard filters
** chr20.hardfiltered.vcf.gz - vcf for whole chromosome after it has been run through hard filters
** chr20.hardfiltered.sites.vcf - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL without the per sample genotypes
** chr20.hardfiltered.sites.vcf - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL without the per sample genotypes
** chr20.hardfiltered.sites.vcf.log - log file
** chr20.hardfiltered.sites.vcf.log - log file
