From a0e134d2ec3ea77caffdea453eae653fd8f96280 Mon Sep 17 00:00:00 2001 From: "Skola, Dylan" Date: Tue, 24 Sep 2019 13:59:28 -0700 Subject: [PATCH] Documentation updates for 0.3.12 release (#110) * Update RELEASES.md (#87) * Updated RELASES.md and normalization.md (#109) --- RELEASES.md | 16 ++++++++++++++++ doc/normalisation.md | 27 ++++++++++++++++++++++++++- 2 files changed, 42 insertions(+), 1 deletion(-) diff --git a/RELEASES.md b/RELEASES.md index 5ef841e..a86c21c 100755 --- a/RELEASES.md +++ b/RELEASES.md @@ -1,10 +1,26 @@ # Hap.py Release Notes / Change Log +## v0.3.12 + +| Ticket | Description | +|---------|------------------------------------------------------------------------------------| +| HAP-355 | Ensure compatibility with genome VCF from DRAGEN pipelines | +| HAP-356 | quantify module throws regex error | +| HAP-357 | Deal with change in Java license terms | +| HAP-359 | Hap.py crashes when ingesting variants genotyped as | +| HAP-360 | Apply non-ref filter to truth set when --preprocess-truth is set | +| HAP-361 | Hap.py "blocksplit" processes still failing on DRAGEN gVCFs even with pre-filtering NON_REF genotypes +| HAP-362 | Hap.py blocksplit sometimes crashes with "invalid next size (fast)" error | +| HAP-363 | Use 'git describe' to obtain version number during Cmake | + ## v0.3.11 | Ticket | Description | |---------|------------------------------------------------------------------------------------| | HAP-341 | Update rtgtools to 3.10.1 | +| HAP-342 | som.py output tables to quantify / GA4GH format | +| HAP-346 | src/sh/illumina-setup.sh out of date | +| HAP-352 | string formatting in som.py: last interval is always [1.0, 1.0] in *extended.csv | ## v0.3.10 diff --git a/doc/normalisation.md b/doc/normalisation.md index 444ab98..74bcc01 100644 --- a/doc/normalisation.md +++ b/doc/normalisation.md @@ -16,7 +16,8 @@ usage: VCF preprocessor [-h] [--location LOCATIONS] [--pass-only] [-T TARGETS_BEDFILE] [-L] [-D] [--bcftools-norm] [--fixchr] [--no-fixchr] [--bcf] [-v] [-r REF] [-w WINDOW] [--threads THREADS] [--force-interactive] - [--logfile LOGFILE] [--verbose | --quiet] + [--logfile LOGFILE] [--verbose | --quiet] [--filter-nonref] + [--convert-gvcf-truth] [--convert-gvcf-query] input output ``` @@ -129,6 +130,30 @@ The default value is 10000, which should be sufficient for short reads. that size are not expected to interfere). ``` +The presence of the symbolic allele in genome VCFs can cause problems +for hap.py, especially if it is part of a genotype. As a workaround, we +provide several options. Since variants genotyped as cannot be +sensibly scored, the we provide the following option, which is safe to use +on both genome VCFs and standard VCFs: + +``` + --filter-nonref Remove any variants genotyped as . + +``` + +If hap.py still crashes when processing a genome VCF, we provide separate +options to perform on-the-fly conversion of a genome VCF to a standard VCF +by removing all alleles and non-variant blocks. Note that this +also removes some fields from the INFO column. These options should only +be used on genome VCFs since attempting to convert a standard VCF will +cause all biallelic variants to be filtered out (most of them). + +``` + --convert-gvcf-truth Convert the truth genome VCF to a standard VCF. + --convert-gvcf-query Convert the query genome VCF to a standard VCF. + +``` + Runtime behaviour can also be controlled as follows: ```