diff --git a/Readme.md b/Readme.md index b1a37c1..4a0a90d 100644 --- a/Readme.md +++ b/Readme.md @@ -250,7 +250,7 @@ The VarDictJava program follows the workflow: 2. Find structural variants (optionally can be disabled by option `-U`). 3. Realign some of the variants using realignment of insertions, deletions, large insertions, and large deletions using unaligned parts of reads (soft-clipped ends). This step is optional and can be disabled using the `-k 0` switch. - 4. Calculate statistics for the variant, filter out some bad ones, if any. + 4. Apply variant filtering rules (hard filters) defined in [Variant filtering](Readme.md#VarFiltering). 5. Assign a type to each variant. 6. Output variants in an intermediate internal format (tabular). Columns of the table are described in the Output Columns section. @@ -301,7 +301,7 @@ String | Description ...^[0-9]+ | something followed by a deletion ...&[ATGC]+ | for insertion/deletion variants followed by a matched sequence -#### Variant Filtering +#### Variant Filtering A variant appears in the output if it satisfies the following criteria (in this order). If variant doesn't fit criteria on the step, it will be filtered out and the next steps won't be checked (except for the step 8, read the explanation below): 1. Frequency of the variant exceeds the threshold set by the `-f` option (default = 1%). diff --git a/VarDict b/VarDict index c74f0b1..f48bf3b 160000 --- a/VarDict +++ b/VarDict @@ -1 +1 @@ -Subproject commit c74f0b19efe1407cdb84a393f76eef13d0f12f17 +Subproject commit f48bf3b0b1c51bc4fd2e6db6b27a7db7f313c846 diff --git a/build.gradle b/build.gradle index ce42236..b0c12d1 100644 --- a/build.gradle +++ b/build.gradle @@ -4,7 +4,7 @@ plugins { id 'jacoco' } -version = '1.8.1' +version = '1.8.2' repositories { mavenCentral() diff --git a/changelog.txt b/changelog.txt index 7af477c..dc68047 100644 --- a/changelog.txt +++ b/changelog.txt @@ -1,3 +1,7 @@ +Version 1.8.2 + - Update Readme.md + - Updated integration tests to vcf 4.2 + Version 1.8.1 - Updated version. - Added validation of VCF files in integration tests. Fixed flag InDelLikely name in expected file and duplicated Bias filter. Updated submodule. diff --git a/tests/integration/expected/vardict.paired.vcf b/tests/integration/expected/vardict.paired.vcf index 53c133b..11416a5 100755 --- a/tests/integration/expected/vardict.paired.vcf +++ b/tests/integration/expected/vardict.paired.vcf @@ -1,5 +1,5 @@ -##fileformat=VCFv4.3 -##source=VarDict_v1.8.1 +##fileformat=VCFv4.2 +##source=VarDict_v1.8.2 ##INFO= ##INFO= ##INFO= diff --git a/tests/integration/expected/vardict.simple.vcf b/tests/integration/expected/vardict.simple.vcf index 383534e..fca6ce4 100755 --- a/tests/integration/expected/vardict.simple.vcf +++ b/tests/integration/expected/vardict.simple.vcf @@ -1,5 +1,5 @@ -##fileformat=VCFv4.3 -##source=VarDict_v1.8.1 +##fileformat=VCFv4.2 +##source=VarDict_v1.8.2 ##INFO= ##INFO= ##INFO=