Instructions for SV variant annotation.

docs_manual/admin_ingest.rst

@@ -68,6 +68,9 @@ First, obtain some tests data for annotation and later import into VarFish Serve
     $ sha256sum --check varfish-test-data-v0.22.2-20210212.tar.gz.sha256
     $ tar -xf varfish-test-data-v0.22.2-20210212.tar.gz.sha256
 
+Annotating Small Variant VCFs
+-----------------------------
+
 Next, you can use the ``varfish-annotator`` command:
 
 .. code-block:: bash
@@ -83,7 +86,7 @@ Next, you can use the ``varfish-annotator`` command:
         --ref-path varfish-annotator-20201006/hs37d5.fa \
         --input-vcf "INPUT.vcf.gz" \
         --release "GRCh37" \
-        --output-db-info "FAM_name.db-info.tsv" \
+        --output-db-info "FAM_name.db-infos.tsv" \
         --output-gts "FAM_name.gts.tsv" \
         --case-id "FAM_name"
 
@@ -181,6 +184,72 @@ For example, if you have genotypes for two siblings but none for the parents:
     FAM_index   father      0       0       1       1
     FAM_index   mother      0       0       2       1
 
+Annotating Structural Variant VCFs
+----------------------------------
+
+Structural variants can be annotated as follows.
+
+
+.. code-block:: bash
+    :linenos:
+
+    $ varfish-annotator \
+        annotate-svs \
+        -XX:MaxHeapSize=10g \
+        -XX:+UseConcMarkSweepGC \
+        \
+        --default-sv-method=YOURCALLERvVERSION"
+        --release GRCh37 \
+        \
+        --db-path varfish-annotator-20201006/varfish-annotator-db-20191129.h2.db \
+        --ensembl-ser-path varfish-annotator-20201006/hg19_ensembl.ser \
+        --refseq-ser-path varfish-annotator-20201006/hg19_refseq_curated.ser \
+        \
+        --input-vcf FAM_sv_calls.vcf.gz \
+        --output-db-info FAM_sv_calls.db-info.tsv \
+        --output-gts FAM_sv_calls.gts.tsv
+        --output-feature-effects CASE_SV_CALLS.feature-effects.tsv
+
+.. note::
+
+    ``varfish-annotator annotate-svs`` will write out the ``INFO/SVMETHOD`` column to the output file.
+    If this value is empty then the value from ``--default-sv-method`` will be used.
+    You **must** either provide ``INFO/SVMETHOD`` or ``--default-sv-method``.
+    Otherwise, you will get errors in the import step (visible in the case import background task view).
+
+    You can use the following shell snippet for adding ``INFO/SVMETHOD`` to your VCF file properly.
+    Replace ``YOURCALLERvVERSION`` with the value that you want to provide to Varfish.
+
+    .. code-block:: shell
+
+        cat >$TMPDIR/header.txt <<"EOF"
+        ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
+        EOF
+
+        bcftools annotate \
+            --header-lines $TMPDIR/header.txt \
+            INPUT.vcf.gz \
+        | awk -F $'\t' '
+            BEGIN { OFS = FS; }
+            /^#/ { print $0; }
+            /^[^#]/ { $8 = $8 ";SVMETHOD=YOURCALLERvVERSION"; print $0; }
+            ' \
+        | bgzip -c \
+        > OUTPUT.vcf.gz
+        tabix -f OUTPUT.vcf.gz
+
+Again, you have have to compress the output TSV files with ``gzip`` and compute MD5 sums.
+
+.. code-block:: bash
+
+    $ gzip -c FAM_sv_calls.db-info.tsv >FAM_sv_calls.db-info.tsv.gz
+    $ md5sum FAM_sv_calls.db-info.tsv.gz >FAM_sv_calls.db-info.tsv.gz.md5
+    $ gzip -c FAM_sv_calls.gts.tsv >FAM_sv_calls.gts.tsv.gz
+    $ md5sum FAM_sv_calls.gts.tsv.gz >FAM_sv_calls.gts.tsv.gz.md5
+    $ gzip -c FAM_sv_calls.feature-effects.tsv >FAM_sv_calls.feature-effects.tsv.gz
+    $ md5sum FAM_sv_calls.feature-effects.tsv.gz >FAM_sv_calls.feature-effectstsv.gz.md5
+
+
 --------------
 Variant Import
 --------------
@@ -214,11 +283,13 @@ When executing the import as shown above, you have to specify:
 
 - a pedigree file with suffix ``.ped``,
 - a genotype annotation file as generated by ``varfish-annotator`` ending in ``.gts.tsv.gz``,
-- a database info file as generated by ``varfish-annotator`` ending in ``.db-infos.tsv.gz``.
+- a database info file as generated by ``varfish-annotator`` ending in ``.db-info.tsv.gz``.
 
 Optionally, you can also specify a TSV file with BAM quality control metris ending in ``.bam-qc.tsv.gz``.
 Currently, the format is not properly documented yet but documentation and supporting tools are forthcoming.
 
+If you want to import structural variants for your case, then you simply submit the output files from the SV annotation step together with the the ``.feature-effects.tsv.gz`` and ``.gts.tsv.gz`` files from the small variant annotation step.
+
 Running the import command through VarFish CLI will create a background import job as shown below.
 Once the job is done, the created or updated case will appear in the case list.