A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
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feat: map primers by bwa and update datavzrd template #275
Primer mapping has been changed from bowtie to bwa mem.
It turned out that bowtie missmaps primers in some rare cases resulting in a loss of reads.
Also the flag for filtering unmapped primers pairs has been fixed. As bowtie just sets the sam flag to 255 filtering was not working as intended.
When mapping primers with bwa two additional parameters need to be set:
-k for setting the minimum seed length which is 19 by default being to high for at least our testcase primers.
-T being the minimum output score (default: 30). This is set to shortest primer - 2 allowing some tolerance when primers are mapped to a different reference.
Further, the datavzrd report has been update to colormap allele frequencies (white to blue) and gnomad af (white to green).
Primer mapping has been changed from bowtie to bwa mem. It turned out that bowtie missmaps primers in some rare cases resulting in a loss of reads. Also the flag for filtering unmapped primers pairs has been fixed. As bowtie just sets the sam flag to 255 filtering was not working as intended. When mapping primers with bwa two additional parameters need to be set:
-kfor setting the minimum seed length which is 19 by default being to high for at least our testcase primers.-Tbeing the minimum output score (default: 30). This is set toshortest primer - 2allowing some tolerance when primers are mapped to a different reference.Further, the datavzrd report has been update to colormap allele frequencies (white to blue) and gnomad af (white to green).