# 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 | |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
]]>