# HG changeset patch # User dfornika # Date 1574726392 0 # Node ID 628c588448324132a1f44026e4d4fefcf86a947e # Parent ae8f5a2e723a9aaaa7f6f011f51360988cd43ec7 Uploaded diff -r ae8f5a2e723a -r 628c58844832 tetyper.xml --- a/tetyper.xml Sat Nov 23 04:19:45 2019 +0000 +++ b/tetyper.xml Mon Nov 25 23:59:52 2019 +0000 @@ -14,6 +14,10 @@ #end if --ref '${reference}' --flank_len '${flank_length}' + --min_reads '${min_reads}' + --min_each_strand '${min_each_strand}' + --min_mapped_len '${min_mapped_len}' + --min_qual '${min_qual}' --outprefix output ]]> @@ -32,7 +36,11 @@ - + + + + + @@ -50,33 +58,33 @@ TETyper will produce a tab-seperated output file with the following outputs: -+---------------+------------------------------------------------+ -| Column | Description | -+===============+================================================+ -| Deletions | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. | -+---------------+------------------------------------------------+ -| Structural_variant | | -+---------------+------------------------------------------------+ -| SNPs_homozygous | | -+---------------+------------------------------------------------+ -| SNPs_heterozygous | | -+---------------+------------------------------------------------+ -| Heterozygous_SNP_counts | | -+---------------+------------------------------------------------+ -| SNP_variant | | -+---------------+------------------------------------------------+ -| Combined_variant | | -+---------------+------------------------------------------------+ -| Left_flanks | | -+---------------+------------------------------------------------+ -| Right_flanks | | -+---------------+------------------------------------------------+ -| Left_flank_counts | | -+---------------+------------------------------------------------+ -| Right_flank_counts | | -+---------------+------------------------------------------------+ -| X_Y_presence | | -+---------------+------------------------------------------------+ ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| Column | Description | ++==========================+==========================================================================================================================================+ +| Deletions | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| Structural_variant | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| SNPs_homozygous | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| SNPs_heterozygous | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| Heterozygous_SNP_counts | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| SNP_variant | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| Combined_variant | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| Left_flanks | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| Right_flanks | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| Left_flank_counts | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| Right_flank_counts | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ +| X_Y_presence | | ++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+ ]]>